Starting phenix.real_space_refine on Mon Mar 11 01:00:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/03_2024/7fdg_31542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/03_2024/7fdg_31542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/03_2024/7fdg_31542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/03_2024/7fdg_31542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/03_2024/7fdg_31542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/03_2024/7fdg_31542.pdb" } resolution = 3.69 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= 0.724 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4134 2.51 5 N 1063 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 615": "OD1" <-> "OD2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 398": "OD1" <-> "OD2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E ASP 420": "OD1" <-> "OD2" Residue "E GLU 484": "OE1" <-> "OE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6459 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4847 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4840 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 597, 4840 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 4968 Chain: "E" Number of atoms: 1542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1573 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" 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: 7.26, per 1000 atoms: 1.12 Number of scatterers: 6459 At special positions: 0 Unit cell: (116.48, 87.36, 80.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1227 8.00 N 1063 7.00 C 4134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.02 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 546 " " NAG A 704 " - " ASN A 90 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 2.2 seconds 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 56.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.896A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.641A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 4.149A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.689A pdb=" N TYR A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.786A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.031A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.616A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 448 through 465 removed outlier: 3.993A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.700A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.332A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.601A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.672A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.216A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.004A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.903A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.709A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.659A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.850A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.652A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 322 hydrogen bonds defined for protein. 916 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: 1.65 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2068 1.35 - 1.47: 1800 1.47 - 1.60: 2721 1.60 - 1.72: 0 1.72 - 1.85: 54 Bond restraints: 6643 Sorted by residual: bond pdb=" C GLY A 319 " pdb=" N LEU A 320 " ideal model delta sigma weight residual 1.329 1.279 0.050 1.86e-02 2.89e+03 7.16e+00 bond pdb=" C VAL A 283 " pdb=" N PRO A 284 " ideal model delta sigma weight residual 1.336 1.308 0.028 1.23e-02 6.61e+03 5.19e+00 bond pdb=" C TYR E 495 " pdb=" N GLY E 496 " ideal model delta sigma weight residual 1.332 1.323 0.009 5.00e-03 4.00e+04 3.39e+00 bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" CA CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sigma weight residual 1.530 1.508 0.022 1.53e-02 4.27e+03 2.13e+00 ... (remaining 6638 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.65: 204 106.65 - 113.49: 3595 113.49 - 120.32: 2555 120.32 - 127.16: 2590 127.16 - 133.99: 94 Bond angle restraints: 9038 Sorted by residual: angle pdb=" C PHE E 464 " pdb=" N GLU E 465 " pdb=" CA GLU E 465 " ideal model delta sigma weight residual 122.93 115.46 7.47 1.45e+00 4.76e-01 2.66e+01 angle pdb=" CA CYS E 379 " pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " ideal model delta sigma weight residual 114.40 123.52 -9.12 2.30e+00 1.89e-01 1.57e+01 angle pdb=" N CYS E 379 " pdb=" CA CYS E 379 " pdb=" C CYS E 379 " ideal model delta sigma weight residual 107.88 113.28 -5.40 1.41e+00 5.03e-01 1.47e+01 angle pdb=" CA PHE E 464 " pdb=" C PHE E 464 " pdb=" N GLU E 465 " ideal model delta sigma weight residual 116.21 120.46 -4.25 1.29e+00 6.01e-01 1.09e+01 angle pdb=" C GLN E 409 " pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 122.59 118.97 3.62 1.10e+00 8.26e-01 1.08e+01 ... (remaining 9033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3501 17.31 - 34.63: 354 34.63 - 51.94: 81 51.94 - 69.26: 29 69.26 - 86.57: 13 Dihedral angle restraints: 3978 sinusoidal: 1649 harmonic: 2329 Sorted by residual: dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 10.31 82.69 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CA VAL E 524 " pdb=" C VAL E 524 " pdb=" N CYS E 525 " pdb=" CA CYS E 525 " ideal model delta harmonic sigma weight residual 180.00 143.31 36.69 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 30.17 62.83 1 1.00e+01 1.00e-02 5.22e+01 ... (remaining 3975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 542 0.035 - 0.071: 290 0.071 - 0.106: 107 0.106 - 0.142: 20 0.142 - 0.177: 3 Chirality restraints: 962 Sorted by residual: chirality pdb=" CA CYS E 379 " pdb=" N CYS E 379 " pdb=" C CYS E 379 " pdb=" CB CYS E 379 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CB ILE E 410 " pdb=" CA ILE E 410 " pdb=" CG1 ILE E 410 " pdb=" CG2 ILE E 410 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 959 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 500 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 283 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 284 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 473 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C TRP A 473 " -0.030 2.00e-02 2.50e+03 pdb=" O TRP A 473 " 0.011 2.00e-02 2.50e+03 pdb=" N MET A 474 " 0.010 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 170 2.63 - 3.20: 6699 3.20 - 3.76: 10796 3.76 - 4.33: 14302 4.33 - 4.90: 21797 Nonbonded interactions: 53764 Sorted by model distance: nonbonded pdb=" O THR A 118 " pdb=" OG1 THR A 122 " model vdw 2.061 2.440 nonbonded pdb=" O ASN A 103 " pdb=" OG SER A 106 " model vdw 2.093 2.440 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR E 500 " model vdw 2.138 2.440 nonbonded pdb=" O HIS A 417 " pdb=" OG SER A 420 " model vdw 2.142 2.440 nonbonded pdb=" O THR A 449 " pdb=" OG1 THR A 453 " model vdw 2.157 2.440 ... (remaining 53759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 3.720 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: 13.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.670 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 6643 Z= 0.422 Angle : 0.848 9.117 9038 Z= 0.487 Chirality : 0.047 0.177 962 Planarity : 0.005 0.044 1166 Dihedral : 16.003 86.573 2465 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.29 % Allowed : 6.55 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.25), residues: 789 helix: -1.83 (0.22), residues: 385 sheet: -1.82 (0.66), residues: 52 loop : -2.73 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 165 HIS 0.006 0.002 HIS A 535 PHE 0.020 0.002 PHE A 400 TYR 0.029 0.002 TYR E 380 ARG 0.006 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.774 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: A 29 LEU cc_start: 0.9484 (mt) cc_final: 0.9248 (mt) REVERT: A 76 GLN cc_start: 0.9324 (mm-40) cc_final: 0.8962 (mm-40) REVERT: A 97 LEU cc_start: 0.9367 (mt) cc_final: 0.9131 (mt) REVERT: A 127 TYR cc_start: 0.6916 (t80) cc_final: 0.6596 (t80) REVERT: A 224 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7900 (mt-10) REVERT: A 249 MET cc_start: 0.7900 (ttp) cc_final: 0.7628 (ttp) REVERT: A 258 PRO cc_start: 0.7916 (Cg_endo) cc_final: 0.7384 (Cg_exo) REVERT: A 362 THR cc_start: 0.8996 (m) cc_final: 0.8775 (m) REVERT: A 406 GLU cc_start: 0.8591 (tt0) cc_final: 0.8372 (tt0) REVERT: A 452 PHE cc_start: 0.9061 (t80) cc_final: 0.8802 (t80) REVERT: A 455 MET cc_start: 0.9132 (tmm) cc_final: 0.8475 (tmm) REVERT: A 481 LYS cc_start: 0.9130 (tppp) cc_final: 0.8662 (ttpt) REVERT: A 485 VAL cc_start: 0.8270 (t) cc_final: 0.7974 (t) REVERT: A 499 ASP cc_start: 0.8617 (m-30) cc_final: 0.8152 (t70) REVERT: A 503 LEU cc_start: 0.8573 (tp) cc_final: 0.8358 (tp) REVERT: E 357 ARG cc_start: 0.8576 (ttt180) cc_final: 0.7204 (mtt180) REVERT: E 418 ILE cc_start: 0.9382 (mp) cc_final: 0.9077 (mp) REVERT: E 455 LEU cc_start: 0.9386 (tp) cc_final: 0.9149 (tp) REVERT: E 481 ASN cc_start: 0.8277 (t0) cc_final: 0.7975 (t0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1968 time to fit residues: 49.3111 Evaluate side-chains 137 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.0070 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 49 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 290 ASN A 338 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS A 552 GLN A 556 ASN E 388 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6643 Z= 0.215 Angle : 0.717 8.358 9038 Z= 0.363 Chirality : 0.046 0.202 962 Planarity : 0.005 0.050 1166 Dihedral : 7.741 59.015 968 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.33 % Allowed : 15.72 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.42 (0.28), residues: 789 helix: 0.01 (0.26), residues: 381 sheet: -1.70 (0.62), residues: 62 loop : -1.85 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 477 HIS 0.004 0.001 HIS A 34 PHE 0.016 0.002 PHE A 369 TYR 0.033 0.002 TYR A 183 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 0.731 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: A 29 LEU cc_start: 0.9488 (mt) cc_final: 0.9244 (mt) REVERT: A 76 GLN cc_start: 0.9298 (mm-40) cc_final: 0.8599 (mm-40) REVERT: A 127 TYR cc_start: 0.6848 (t80) cc_final: 0.6618 (t80) REVERT: A 249 MET cc_start: 0.8047 (ttp) cc_final: 0.7812 (ttp) REVERT: A 258 PRO cc_start: 0.7786 (Cg_endo) cc_final: 0.7330 (Cg_exo) REVERT: A 323 MET cc_start: 0.8013 (mmm) cc_final: 0.7106 (mmm) REVERT: A 353 LYS cc_start: 0.9032 (mttt) cc_final: 0.8134 (ttmt) REVERT: A 360 MET cc_start: 0.7692 (tmm) cc_final: 0.7069 (tpt) REVERT: A 455 MET cc_start: 0.8874 (tmm) cc_final: 0.8405 (tmm) REVERT: A 477 TRP cc_start: 0.7002 (t-100) cc_final: 0.6625 (t-100) REVERT: A 481 LYS cc_start: 0.8934 (tppp) cc_final: 0.8622 (ttpt) REVERT: E 357 ARG cc_start: 0.8438 (ttt180) cc_final: 0.7102 (mtt180) REVERT: E 409 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8666 (mp10) REVERT: E 444 LYS cc_start: 0.8038 (ptmm) cc_final: 0.7540 (ptpp) outliers start: 14 outliers final: 8 residues processed: 190 average time/residue: 0.1697 time to fit residues: 43.1090 Evaluate side-chains 161 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 76 GLN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN E 414 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6643 Z= 0.250 Angle : 0.716 7.570 9038 Z= 0.361 Chirality : 0.046 0.259 962 Planarity : 0.005 0.047 1166 Dihedral : 7.450 58.727 968 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.77 % Allowed : 18.78 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.02 (0.29), residues: 789 helix: 0.29 (0.26), residues: 387 sheet: -1.61 (0.64), residues: 60 loop : -1.61 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 477 HIS 0.008 0.001 HIS A 265 PHE 0.024 0.002 PHE A 274 TYR 0.025 0.002 TYR A 381 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 0.710 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: A 72 PHE cc_start: 0.8916 (t80) cc_final: 0.8668 (t80) REVERT: A 76 GLN cc_start: 0.9165 (mm110) cc_final: 0.8705 (mm-40) REVERT: A 127 TYR cc_start: 0.6869 (t80) cc_final: 0.6604 (t80) REVERT: A 249 MET cc_start: 0.8124 (ttp) cc_final: 0.7832 (ttp) REVERT: A 258 PRO cc_start: 0.7760 (Cg_endo) cc_final: 0.7275 (Cg_exo) REVERT: A 323 MET cc_start: 0.7871 (mmm) cc_final: 0.6966 (mmm) REVERT: A 353 LYS cc_start: 0.9059 (mttt) cc_final: 0.8246 (ttmt) REVERT: A 360 MET cc_start: 0.7823 (tmm) cc_final: 0.7398 (tpt) REVERT: A 376 MET cc_start: 0.9101 (mmm) cc_final: 0.8800 (tpt) REVERT: A 481 LYS cc_start: 0.8955 (tppp) cc_final: 0.8671 (ttpt) REVERT: E 357 ARG cc_start: 0.8323 (ttt180) cc_final: 0.7012 (mtt180) REVERT: E 423 TYR cc_start: 0.8571 (t80) cc_final: 0.7793 (t80) REVERT: E 444 LYS cc_start: 0.8201 (ptmm) cc_final: 0.6513 (mttt) REVERT: E 473 TYR cc_start: 0.8570 (t80) cc_final: 0.8197 (t80) outliers start: 17 outliers final: 11 residues processed: 174 average time/residue: 0.1817 time to fit residues: 41.9355 Evaluate side-chains 163 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 0.0570 chunk 42 optimal weight: 0.0980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6643 Z= 0.208 Angle : 0.709 9.089 9038 Z= 0.350 Chirality : 0.044 0.152 962 Planarity : 0.004 0.050 1166 Dihedral : 6.727 54.691 968 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.77 % Allowed : 20.38 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.67 (0.29), residues: 789 helix: 0.58 (0.26), residues: 387 sheet: -1.39 (0.67), residues: 60 loop : -1.43 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 477 HIS 0.004 0.001 HIS A 34 PHE 0.032 0.002 PHE A 452 TYR 0.029 0.002 TYR A 381 ARG 0.005 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 0.833 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 72 PHE cc_start: 0.8867 (t80) cc_final: 0.8566 (t80) REVERT: A 127 TYR cc_start: 0.6899 (t80) cc_final: 0.6694 (t80) REVERT: A 258 PRO cc_start: 0.7784 (Cg_endo) cc_final: 0.7355 (Cg_exo) REVERT: A 323 MET cc_start: 0.7763 (mmm) cc_final: 0.6921 (mmm) REVERT: A 353 LYS cc_start: 0.8870 (mttt) cc_final: 0.7975 (ttmt) REVERT: A 376 MET cc_start: 0.9034 (mmm) cc_final: 0.8682 (tpt) REVERT: A 392 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8442 (mm) REVERT: A 406 GLU cc_start: 0.8600 (tt0) cc_final: 0.8312 (tt0) REVERT: A 481 LYS cc_start: 0.8928 (tppp) cc_final: 0.8678 (ttpt) REVERT: A 483 GLU cc_start: 0.8902 (tp30) cc_final: 0.8696 (mm-30) REVERT: A 565 PRO cc_start: 0.8586 (Cg_exo) cc_final: 0.8343 (Cg_endo) REVERT: E 357 ARG cc_start: 0.8291 (ttt180) cc_final: 0.6997 (mtt180) REVERT: E 423 TYR cc_start: 0.8522 (t80) cc_final: 0.7728 (t80) REVERT: E 444 LYS cc_start: 0.8211 (ptmm) cc_final: 0.6486 (mttt) REVERT: E 473 TYR cc_start: 0.8509 (t80) cc_final: 0.8176 (t80) outliers start: 17 outliers final: 13 residues processed: 181 average time/residue: 0.2126 time to fit residues: 50.7846 Evaluate side-chains 165 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6643 Z= 0.311 Angle : 0.735 8.447 9038 Z= 0.376 Chirality : 0.045 0.144 962 Planarity : 0.005 0.049 1166 Dihedral : 6.925 59.898 968 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.49 % Allowed : 21.69 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.78 (0.30), residues: 789 helix: 0.50 (0.26), residues: 389 sheet: -1.56 (0.68), residues: 60 loop : -1.49 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 477 HIS 0.006 0.001 HIS A 378 PHE 0.035 0.002 PHE E 456 TYR 0.030 0.002 TYR A 381 ARG 0.003 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.983 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: A 72 PHE cc_start: 0.8943 (t80) cc_final: 0.8624 (t80) REVERT: A 258 PRO cc_start: 0.7684 (Cg_endo) cc_final: 0.7417 (Cg_exo) REVERT: A 323 MET cc_start: 0.7849 (mmm) cc_final: 0.7142 (mmm) REVERT: A 353 LYS cc_start: 0.8993 (mttt) cc_final: 0.8025 (ttmt) REVERT: A 376 MET cc_start: 0.9110 (mmm) cc_final: 0.8728 (tpt) REVERT: A 392 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8489 (mm) REVERT: A 481 LYS cc_start: 0.8934 (tppp) cc_final: 0.8608 (ttmm) REVERT: A 483 GLU cc_start: 0.8966 (tp30) cc_final: 0.8642 (mm-30) REVERT: A 515 TYR cc_start: 0.8551 (m-80) cc_final: 0.7804 (m-10) REVERT: A 518 ARG cc_start: 0.8679 (tmm-80) cc_final: 0.8278 (tmm-80) REVERT: A 565 PRO cc_start: 0.8845 (Cg_exo) cc_final: 0.8607 (Cg_endo) REVERT: E 357 ARG cc_start: 0.8332 (ttt180) cc_final: 0.7065 (mtt180) REVERT: E 444 LYS cc_start: 0.8313 (ptmm) cc_final: 0.6546 (mttt) outliers start: 23 outliers final: 17 residues processed: 163 average time/residue: 0.1929 time to fit residues: 41.5267 Evaluate side-chains 157 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 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 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6643 Z= 0.205 Angle : 0.714 9.944 9038 Z= 0.357 Chirality : 0.044 0.179 962 Planarity : 0.004 0.052 1166 Dihedral : 6.289 56.503 968 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.64 % Allowed : 22.42 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.51 (0.30), residues: 789 helix: 0.64 (0.26), residues: 392 sheet: -1.30 (0.69), residues: 62 loop : -1.27 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 477 HIS 0.005 0.001 HIS A 34 PHE 0.039 0.002 PHE A 452 TYR 0.028 0.002 TYR A 381 ARG 0.002 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 0.754 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: A 72 PHE cc_start: 0.8902 (t80) cc_final: 0.8509 (t80) REVERT: A 75 GLU cc_start: 0.8213 (pp20) cc_final: 0.7734 (pp20) REVERT: A 76 GLN cc_start: 0.9018 (mm110) cc_final: 0.8746 (mm-40) REVERT: A 258 PRO cc_start: 0.7356 (Cg_endo) cc_final: 0.7011 (Cg_exo) REVERT: A 323 MET cc_start: 0.7783 (mmm) cc_final: 0.7126 (mmm) REVERT: A 353 LYS cc_start: 0.8909 (mttt) cc_final: 0.7959 (ttmt) REVERT: A 376 MET cc_start: 0.9056 (mmm) cc_final: 0.8699 (tpt) REVERT: A 392 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 481 LYS cc_start: 0.8893 (tppp) cc_final: 0.8610 (ttmm) REVERT: A 483 GLU cc_start: 0.8887 (tp30) cc_final: 0.8620 (mm-30) REVERT: A 499 ASP cc_start: 0.8434 (m-30) cc_final: 0.7778 (t70) REVERT: A 565 PRO cc_start: 0.8704 (Cg_exo) cc_final: 0.8476 (Cg_endo) REVERT: E 357 ARG cc_start: 0.8275 (ttt180) cc_final: 0.6985 (mtt180) REVERT: E 444 LYS cc_start: 0.8270 (ptmm) cc_final: 0.6537 (mttt) REVERT: E 473 TYR cc_start: 0.8523 (t80) cc_final: 0.8169 (t80) outliers start: 24 outliers final: 18 residues processed: 169 average time/residue: 0.1950 time to fit residues: 43.7323 Evaluate side-chains 163 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6643 Z= 0.219 Angle : 0.692 8.535 9038 Z= 0.346 Chirality : 0.043 0.140 962 Planarity : 0.004 0.051 1166 Dihedral : 6.095 55.439 968 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.35 % Allowed : 22.85 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.47 (0.30), residues: 789 helix: 0.64 (0.26), residues: 399 sheet: -0.86 (0.73), residues: 57 loop : -1.35 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.029 0.002 PHE A 452 TYR 0.027 0.002 TYR A 381 ARG 0.002 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 0.745 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: A 58 ASN cc_start: 0.8450 (t0) cc_final: 0.8148 (t0) REVERT: A 72 PHE cc_start: 0.8916 (t80) cc_final: 0.8503 (t80) REVERT: A 75 GLU cc_start: 0.8286 (pp20) cc_final: 0.7792 (pp20) REVERT: A 76 GLN cc_start: 0.9077 (mm110) cc_final: 0.8823 (mm-40) REVERT: A 258 PRO cc_start: 0.7422 (Cg_endo) cc_final: 0.7091 (Cg_exo) REVERT: A 323 MET cc_start: 0.7713 (mmm) cc_final: 0.7059 (mmm) REVERT: A 353 LYS cc_start: 0.9008 (mttt) cc_final: 0.8007 (ttmt) REVERT: A 376 MET cc_start: 0.9067 (mmm) cc_final: 0.8687 (tpt) REVERT: A 392 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8349 (mm) REVERT: A 481 LYS cc_start: 0.8886 (tppp) cc_final: 0.8590 (ttmm) REVERT: A 499 ASP cc_start: 0.8422 (m-30) cc_final: 0.7999 (t70) REVERT: A 565 PRO cc_start: 0.8765 (Cg_exo) cc_final: 0.8539 (Cg_endo) REVERT: E 357 ARG cc_start: 0.8258 (ttt180) cc_final: 0.7018 (mtt180) REVERT: E 444 LYS cc_start: 0.8331 (ptmm) cc_final: 0.6591 (mttt) outliers start: 22 outliers final: 17 residues processed: 166 average time/residue: 0.1872 time to fit residues: 41.0561 Evaluate side-chains 163 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.0050 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6643 Z= 0.207 Angle : 0.711 11.111 9038 Z= 0.354 Chirality : 0.043 0.168 962 Planarity : 0.005 0.052 1166 Dihedral : 5.917 53.908 968 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.20 % Allowed : 23.73 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.30 (0.31), residues: 789 helix: 0.69 (0.26), residues: 399 sheet: -0.82 (0.75), residues: 53 loop : -1.13 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.037 0.002 PHE A 274 TYR 0.028 0.002 TYR A 381 ARG 0.005 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8501 (t0) cc_final: 0.8199 (t0) REVERT: A 62 MET cc_start: 0.9257 (ttp) cc_final: 0.8998 (ttp) REVERT: A 72 PHE cc_start: 0.8893 (t80) cc_final: 0.8469 (t80) REVERT: A 75 GLU cc_start: 0.8309 (pp20) cc_final: 0.7777 (pp20) REVERT: A 76 GLN cc_start: 0.9099 (mm110) cc_final: 0.8837 (mm-40) REVERT: A 258 PRO cc_start: 0.7507 (Cg_endo) cc_final: 0.7180 (Cg_exo) REVERT: A 297 MET cc_start: 0.8227 (tpp) cc_final: 0.7935 (tpp) REVERT: A 323 MET cc_start: 0.7624 (mmm) cc_final: 0.7113 (mmm) REVERT: A 353 LYS cc_start: 0.8983 (mttt) cc_final: 0.7966 (ttmt) REVERT: A 392 LEU cc_start: 0.8657 (mm) cc_final: 0.8270 (mm) REVERT: A 406 GLU cc_start: 0.8591 (tt0) cc_final: 0.8297 (tt0) REVERT: A 481 LYS cc_start: 0.8873 (tppp) cc_final: 0.8603 (ttmm) REVERT: A 565 PRO cc_start: 0.8776 (Cg_exo) cc_final: 0.8554 (Cg_endo) REVERT: E 357 ARG cc_start: 0.8173 (ttt180) cc_final: 0.6964 (mtt180) REVERT: E 444 LYS cc_start: 0.8338 (ptmm) cc_final: 0.6654 (mttt) outliers start: 21 outliers final: 19 residues processed: 160 average time/residue: 0.1818 time to fit residues: 38.9891 Evaluate side-chains 162 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.174 6643 Z= 0.478 Angle : 1.157 59.197 9038 Z= 0.657 Chirality : 0.051 0.470 962 Planarity : 0.006 0.113 1166 Dihedral : 5.942 53.904 968 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.20 % Allowed : 24.60 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.33 (0.31), residues: 789 helix: 0.71 (0.26), residues: 399 sheet: -0.79 (0.72), residues: 59 loop : -1.22 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP A 168 HIS 0.007 0.001 HIS A 34 PHE 0.023 0.002 PHE A 274 TYR 0.027 0.002 TYR A 381 ARG 0.006 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8504 (t0) cc_final: 0.8202 (t0) REVERT: A 62 MET cc_start: 0.9256 (ttp) cc_final: 0.8996 (ttp) REVERT: A 72 PHE cc_start: 0.8900 (t80) cc_final: 0.8471 (t80) REVERT: A 75 GLU cc_start: 0.8273 (pp20) cc_final: 0.7795 (pp20) REVERT: A 76 GLN cc_start: 0.9099 (mm110) cc_final: 0.8839 (mm-40) REVERT: A 258 PRO cc_start: 0.7507 (Cg_endo) cc_final: 0.7183 (Cg_exo) REVERT: A 297 MET cc_start: 0.8231 (tpp) cc_final: 0.7933 (tpp) REVERT: A 323 MET cc_start: 0.7597 (mmm) cc_final: 0.6673 (mmm) REVERT: A 353 LYS cc_start: 0.8997 (mttt) cc_final: 0.7970 (ttmt) REVERT: A 392 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8270 (mm) REVERT: A 406 GLU cc_start: 0.8592 (tt0) cc_final: 0.8301 (tt0) REVERT: A 435 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7714 (mm-30) REVERT: A 481 LYS cc_start: 0.8878 (tppp) cc_final: 0.8606 (ttmm) REVERT: A 565 PRO cc_start: 0.8773 (Cg_exo) cc_final: 0.8516 (Cg_endo) REVERT: E 357 ARG cc_start: 0.8173 (ttt180) cc_final: 0.6971 (mtt180) REVERT: E 444 LYS cc_start: 0.8333 (ptmm) cc_final: 0.6657 (mttt) outliers start: 21 outliers final: 18 residues processed: 154 average time/residue: 0.1734 time to fit residues: 36.2896 Evaluate side-chains 162 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0570 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 49 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.0670 chunk 9 optimal weight: 5.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.174 6643 Z= 0.478 Angle : 1.157 59.197 9038 Z= 0.657 Chirality : 0.051 0.470 962 Planarity : 0.006 0.113 1166 Dihedral : 5.942 53.904 968 Min Nonbonded Distance : 1.064 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.91 % Allowed : 24.89 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.33 (0.31), residues: 789 helix: 0.71 (0.26), residues: 399 sheet: -0.79 (0.72), residues: 59 loop : -1.22 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP A 168 HIS 0.007 0.001 HIS A 34 PHE 0.023 0.002 PHE A 274 TYR 0.027 0.002 TYR A 381 ARG 0.006 0.001 ARG E 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8505 (t0) cc_final: 0.8202 (t0) REVERT: A 62 MET cc_start: 0.9254 (ttp) cc_final: 0.8995 (ttp) REVERT: A 72 PHE cc_start: 0.8901 (t80) cc_final: 0.8471 (t80) REVERT: A 75 GLU cc_start: 0.8300 (pp20) cc_final: 0.7796 (pp20) REVERT: A 76 GLN cc_start: 0.9096 (mm110) cc_final: 0.8839 (mm-40) REVERT: A 258 PRO cc_start: 0.7505 (Cg_endo) cc_final: 0.7183 (Cg_exo) REVERT: A 297 MET cc_start: 0.8230 (tpp) cc_final: 0.7933 (tpp) REVERT: A 323 MET cc_start: 0.7715 (mmm) cc_final: 0.6909 (mmm) REVERT: A 353 LYS cc_start: 0.9001 (mttt) cc_final: 0.7971 (ttmt) REVERT: A 392 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8270 (mm) REVERT: A 406 GLU cc_start: 0.8591 (tt0) cc_final: 0.8301 (tt0) REVERT: A 435 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7714 (mm-30) REVERT: A 481 LYS cc_start: 0.8873 (tppp) cc_final: 0.8606 (ttmm) REVERT: A 565 PRO cc_start: 0.8775 (Cg_exo) cc_final: 0.8516 (Cg_endo) REVERT: E 357 ARG cc_start: 0.8172 (ttt180) cc_final: 0.6971 (mtt180) REVERT: E 444 LYS cc_start: 0.8333 (ptmm) cc_final: 0.6657 (mttt) outliers start: 19 outliers final: 18 residues processed: 152 average time/residue: 0.1856 time to fit residues: 37.9904 Evaluate side-chains 163 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.4980 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 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 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.117697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.099126 restraints weight = 33681.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.103574 restraints weight = 14559.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106516 restraints weight = 8094.423| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.174 6643 Z= 0.478 Angle : 1.157 59.197 9038 Z= 0.657 Chirality : 0.051 0.470 962 Planarity : 0.006 0.113 1166 Dihedral : 5.942 53.904 968 Min Nonbonded Distance : 1.192 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.91 % Allowed : 24.89 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.33 (0.31), residues: 789 helix: 0.71 (0.26), residues: 399 sheet: -0.79 (0.72), residues: 59 loop : -1.22 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP A 168 HIS 0.007 0.001 HIS A 34 PHE 0.023 0.002 PHE A 274 TYR 0.027 0.002 TYR A 381 ARG 0.006 0.001 ARG E 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.93 seconds wall clock time: 34 minutes 27.84 seconds (2067.84 seconds total)