Starting phenix.real_space_refine on Mon Sep 23 20:39:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yqq_39502/09_2024/8yqq_39502_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yqq_39502/09_2024/8yqq_39502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yqq_39502/09_2024/8yqq_39502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yqq_39502/09_2024/8yqq_39502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yqq_39502/09_2024/8yqq_39502_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yqq_39502/09_2024/8yqq_39502_trim.cif" } resolution = 3.95 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= 0.002 sd= 0.031 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 47 5.16 5 C 3217 2.51 5 N 883 2.21 5 O 994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2218 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 267} Chain: "B" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2833 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 346} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.79, per 1000 atoms: 0.74 Number of scatterers: 5141 At special positions: 0 Unit cell: (68.04, 80.19, 134.46, 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 47 16.00 O 994 8.00 N 883 7.00 C 3217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.02 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.02 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.02 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=1.99 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=1.99 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=1.98 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=1.99 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.01 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.00 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.01 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 465 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 703 " - " ASN A 355 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 631.2 milliseconds 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1204 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 12 sheets defined 13.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.681A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 4.023A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.720A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 400 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 430 through 434 removed outlier: 4.180A pdb=" N VAL A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.708A pdb=" N VAL A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.097A pdb=" N PHE A 572 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.951A pdb=" N GLY B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 183 " --> pdb=" O ASN B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 480 through 491 removed outlier: 3.519A pdb=" N TYR B 485 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 371 removed outlier: 6.282A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.686A pdb=" N PHE A 391 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 459 through 463 removed outlier: 4.225A pdb=" N ASP A 578 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 576 " --> pdb=" O TYR A 462 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.396A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 509 removed outlier: 6.502A pdb=" N THR A 509 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.504A pdb=" N ARG B 150 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 167 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 200 Processing sheet with id=AB1, first strand: chain 'B' and resid 209 through 211 Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 275 removed outlier: 3.744A pdb=" N CYS B 281 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 275 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N HIS B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 348 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL B 331 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS B 350 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 328 " --> pdb=" O TRP B 308 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N TRP B 308 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 378 through 383 removed outlier: 4.250A pdb=" N CYS B 426 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL B 473 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 460 " --> pdb=" O VAL B 473 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 447 " --> pdb=" O TRP B 454 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 445 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 382 " --> pdb=" O PRO B 444 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER B 448 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU B 378 " --> pdb=" O SER B 448 " (cutoff:3.500A) 109 hydrogen bonds defined for protein. 270 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: 1.39 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 885 1.32 - 1.45: 1510 1.45 - 1.57: 2825 1.57 - 1.70: 0 1.70 - 1.83: 56 Bond restraints: 5276 Sorted by residual: bond pdb=" CA SER A 563 " pdb=" CB SER A 563 " ideal model delta sigma weight residual 1.533 1.450 0.083 1.69e-02 3.50e+03 2.40e+01 bond pdb=" C PRO A 496 " pdb=" O PRO A 496 " ideal model delta sigma weight residual 1.233 1.194 0.039 9.90e-03 1.02e+04 1.56e+01 bond pdb=" N ILE A 588 " pdb=" CA ILE A 588 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.11e-02 8.12e+03 1.45e+01 bond pdb=" CA SER A 488 " pdb=" CB SER A 488 " ideal model delta sigma weight residual 1.531 1.476 0.055 1.53e-02 4.27e+03 1.31e+01 bond pdb=" C PRO A 490 " pdb=" O PRO A 490 " ideal model delta sigma weight residual 1.240 1.200 0.040 1.12e-02 7.97e+03 1.30e+01 ... (remaining 5271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 6625 2.37 - 4.74: 479 4.74 - 7.11: 65 7.11 - 9.48: 11 9.48 - 11.85: 3 Bond angle restraints: 7183 Sorted by residual: angle pdb=" N ARG A 447 " pdb=" CA ARG A 447 " pdb=" C ARG A 447 " ideal model delta sigma weight residual 113.50 103.12 10.38 1.23e+00 6.61e-01 7.12e+01 angle pdb=" N PRO A 475 " pdb=" CA PRO A 475 " pdb=" C PRO A 475 " ideal model delta sigma weight residual 113.75 104.29 9.46 1.49e+00 4.50e-01 4.03e+01 angle pdb=" C THR A 602 " pdb=" CA THR A 602 " pdb=" CB THR A 602 " ideal model delta sigma weight residual 111.74 103.25 8.49 1.37e+00 5.33e-01 3.84e+01 angle pdb=" N GLN A 559 " pdb=" CA GLN A 559 " pdb=" C GLN A 559 " ideal model delta sigma weight residual 113.41 106.01 7.40 1.22e+00 6.72e-01 3.68e+01 angle pdb=" CA HIS A 562 " pdb=" CB HIS A 562 " pdb=" CG HIS A 562 " ideal model delta sigma weight residual 113.80 119.33 -5.53 1.00e+00 1.00e+00 3.06e+01 ... (remaining 7178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 2963 23.97 - 47.94: 241 47.94 - 71.91: 41 71.91 - 95.87: 6 95.87 - 119.84: 4 Dihedral angle restraints: 3255 sinusoidal: 1380 harmonic: 1875 Sorted by residual: dihedral pdb=" CD ARG A 517 " pdb=" NE ARG A 517 " pdb=" CZ ARG A 517 " pdb=" NH1 ARG A 517 " ideal model delta sinusoidal sigma weight residual 0.00 86.60 -86.60 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS A 485 " pdb=" SG CYS A 485 " pdb=" SG CYS A 516 " pdb=" CB CYS A 516 " ideal model delta sinusoidal sigma weight residual 93.00 156.79 -63.79 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CD ARG A 585 " pdb=" NE ARG A 585 " pdb=" CZ ARG A 585 " pdb=" NH1 ARG A 585 " ideal model delta sinusoidal sigma weight residual 0.00 60.32 -60.32 1 1.00e+01 1.00e-02 4.85e+01 ... (remaining 3252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 560 0.069 - 0.139: 171 0.139 - 0.208: 43 0.208 - 0.278: 7 0.278 - 0.347: 1 Chirality restraints: 782 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 355 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ARG A 447 " pdb=" N ARG A 447 " pdb=" C ARG A 447 " pdb=" CB ARG A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ASN A 598 " pdb=" N ASN A 598 " pdb=" C ASN A 598 " pdb=" CB ASN A 598 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 779 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 355 " 0.115 2.00e-02 2.50e+03 4.11e-01 2.11e+03 pdb=" CG ASN A 355 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN A 355 " 0.401 2.00e-02 2.50e+03 pdb=" ND2 ASN A 355 " -0.756 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.308 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " 0.347 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG B 502 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " 0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " -0.346 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG A 701 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " -0.113 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " -0.156 2.00e-02 2.50e+03 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 3 2.14 - 2.83: 1695 2.83 - 3.52: 6799 3.52 - 4.21: 12060 4.21 - 4.90: 19794 Nonbonded interactions: 40351 Sorted by model distance: nonbonded pdb=" O3 NAG B 501 " pdb=" O5 NAG B 502 " model vdw 1.447 3.040 nonbonded pdb=" O ASN A 605 " pdb=" N LEU A 607 " model vdw 1.913 3.120 nonbonded pdb=" O3 NAG B 501 " pdb=" C1 NAG B 502 " model vdw 2.079 3.470 nonbonded pdb=" OE1 GLU B 178 " pdb=" OG SER B 197 " model vdw 2.250 3.040 nonbonded pdb=" OE2 GLU B 299 " pdb=" OH TYR B 337 " model vdw 2.263 3.040 ... (remaining 40346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.008 0.083 5276 Z= 0.536 Angle : 1.283 11.846 7183 Z= 0.833 Chirality : 0.073 0.347 782 Planarity : 0.036 0.495 929 Dihedral : 17.141 119.842 1997 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 2.79 % Allowed : 9.92 % Favored : 87.29 % Rotamer: Outliers : 8.03 % Allowed : 12.39 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.30), residues: 645 helix: -3.36 (0.40), residues: 69 sheet: -0.95 (0.47), residues: 132 loop : -2.37 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 269 HIS 0.006 0.001 HIS A 562 PHE 0.026 0.002 PHE A 383 TYR 0.031 0.002 TYR A 501 ARG 0.012 0.001 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 120 time to evaluate : 0.627 Fit side-chains REVERT: A 337 SER cc_start: 0.9441 (m) cc_final: 0.9094 (t) REVERT: A 410 GLN cc_start: 0.7969 (mm110) cc_final: 0.7715 (mt0) REVERT: A 517 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7787 (mtm-85) REVERT: A 538 VAL cc_start: 0.9538 (OUTLIER) cc_final: 0.9338 (t) REVERT: A 544 GLU cc_start: 0.8893 (mp0) cc_final: 0.8644 (mp0) REVERT: A 552 ASN cc_start: 0.9140 (t0) cc_final: 0.8784 (t0) REVERT: A 581 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8177 (mt) REVERT: A 602 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8770 (t) REVERT: A 604 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8202 (m) REVERT: A 606 ASP cc_start: 0.8625 (m-30) cc_final: 0.8352 (m-30) REVERT: B 268 PRO cc_start: 0.8464 (Cg_endo) cc_final: 0.8187 (Cg_exo) REVERT: B 463 SER cc_start: 0.8674 (t) cc_final: 0.8389 (p) outliers start: 46 outliers final: 24 residues processed: 150 average time/residue: 0.1627 time to fit residues: 31.4084 Evaluate side-chains 115 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 556 CYS Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 604 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 0.0970 chunk 58 optimal weight: 0.0020 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN A 562 HIS A 587 ASN A 598 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5276 Z= 0.192 Angle : 0.710 16.054 7183 Z= 0.346 Chirality : 0.053 0.627 782 Planarity : 0.005 0.059 929 Dihedral : 9.442 57.173 893 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.51 % Favored : 93.18 % Rotamer: Outliers : 3.66 % Allowed : 17.80 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.31), residues: 645 helix: -2.49 (0.44), residues: 70 sheet: -1.68 (0.41), residues: 155 loop : -1.62 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 269 HIS 0.003 0.001 HIS B 227 PHE 0.021 0.002 PHE A 577 TYR 0.020 0.002 TYR A 458 ARG 0.005 0.001 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.610 Fit side-chains REVERT: A 502 ARG cc_start: 0.8269 (ptp-170) cc_final: 0.8052 (ptp-170) REVERT: A 538 VAL cc_start: 0.9397 (m) cc_final: 0.9178 (t) REVERT: A 544 GLU cc_start: 0.8847 (mp0) cc_final: 0.8597 (mp0) REVERT: A 562 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.6941 (m170) REVERT: A 578 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: B 151 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8690 (mm) REVERT: B 188 MET cc_start: 0.6496 (ttm) cc_final: 0.6279 (ttp) REVERT: B 268 PRO cc_start: 0.8511 (Cg_endo) cc_final: 0.8268 (Cg_exo) REVERT: B 458 ASP cc_start: 0.8706 (t0) cc_final: 0.8404 (t0) REVERT: B 463 SER cc_start: 0.8704 (t) cc_final: 0.8403 (p) REVERT: B 488 MET cc_start: 0.8533 (mmt) cc_final: 0.6859 (mmt) outliers start: 21 outliers final: 14 residues processed: 108 average time/residue: 0.1477 time to fit residues: 21.3050 Evaluate side-chains 91 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 TRP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN A 595 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5276 Z= 0.208 Angle : 0.675 16.041 7183 Z= 0.329 Chirality : 0.053 0.650 782 Planarity : 0.005 0.053 929 Dihedral : 8.414 59.754 864 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.29 % Favored : 92.56 % Rotamer: Outliers : 3.32 % Allowed : 20.07 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.32), residues: 645 helix: -1.90 (0.50), residues: 70 sheet: -1.78 (0.40), residues: 155 loop : -1.20 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 269 HIS 0.008 0.002 HIS A 562 PHE 0.017 0.002 PHE A 577 TYR 0.017 0.002 TYR A 426 ARG 0.004 0.001 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.584 Fit side-chains REVERT: A 413 ASN cc_start: 0.8500 (m-40) cc_final: 0.8263 (m-40) REVERT: A 544 GLU cc_start: 0.8837 (mp0) cc_final: 0.8633 (mp0) REVERT: B 231 CYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8109 (m) REVERT: B 268 PRO cc_start: 0.8512 (Cg_endo) cc_final: 0.8229 (Cg_exo) REVERT: B 384 TRP cc_start: 0.8901 (m-90) cc_final: 0.8658 (m-90) REVERT: B 458 ASP cc_start: 0.8666 (t0) cc_final: 0.8334 (t0) REVERT: B 463 SER cc_start: 0.8735 (t) cc_final: 0.8476 (p) outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 0.1628 time to fit residues: 21.2224 Evaluate side-chains 83 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5276 Z= 0.221 Angle : 0.648 15.253 7183 Z= 0.319 Chirality : 0.053 0.646 782 Planarity : 0.004 0.050 929 Dihedral : 7.814 58.528 853 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.67 % Favored : 93.18 % Rotamer: Outliers : 3.66 % Allowed : 20.59 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.84 (0.32), residues: 645 helix: -1.25 (0.59), residues: 63 sheet: -1.54 (0.40), residues: 160 loop : -1.07 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 176 HIS 0.004 0.001 HIS A 465 PHE 0.018 0.002 PHE A 577 TYR 0.017 0.002 TYR A 426 ARG 0.003 0.001 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 GLN cc_start: 0.7669 (mm110) cc_final: 0.7362 (mt0) REVERT: A 413 ASN cc_start: 0.8531 (m-40) cc_final: 0.8289 (m-40) REVERT: A 555 LYS cc_start: 0.9005 (mttp) cc_final: 0.8776 (mttp) REVERT: B 157 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7491 (mt) REVERT: B 268 PRO cc_start: 0.8495 (Cg_endo) cc_final: 0.8206 (Cg_exo) REVERT: B 293 THR cc_start: 0.8667 (t) cc_final: 0.8453 (t) REVERT: B 458 ASP cc_start: 0.8659 (t0) cc_final: 0.8371 (t0) REVERT: B 463 SER cc_start: 0.8769 (t) cc_final: 0.8296 (p) outliers start: 21 outliers final: 13 residues processed: 96 average time/residue: 0.1964 time to fit residues: 23.9940 Evaluate side-chains 89 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 0.2980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5276 Z= 0.157 Angle : 0.591 11.541 7183 Z= 0.294 Chirality : 0.051 0.617 782 Planarity : 0.004 0.048 929 Dihedral : 7.500 57.800 853 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.12 % Favored : 94.73 % Rotamer: Outliers : 3.49 % Allowed : 20.24 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.67 (0.32), residues: 645 helix: -0.98 (0.62), residues: 63 sheet: -1.34 (0.40), residues: 160 loop : -1.02 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 269 HIS 0.002 0.001 HIS A 465 PHE 0.019 0.001 PHE B 311 TYR 0.014 0.001 TYR A 528 ARG 0.003 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASN cc_start: 0.8500 (m-40) cc_final: 0.8266 (m-40) REVERT: A 525 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 540 VAL cc_start: 0.9495 (OUTLIER) cc_final: 0.9263 (p) REVERT: B 157 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7376 (mt) REVERT: B 268 PRO cc_start: 0.8514 (Cg_endo) cc_final: 0.8248 (Cg_exo) REVERT: B 293 THR cc_start: 0.8613 (t) cc_final: 0.8379 (t) REVERT: B 458 ASP cc_start: 0.8609 (t0) cc_final: 0.8355 (t0) REVERT: B 463 SER cc_start: 0.8833 (t) cc_final: 0.8250 (p) REVERT: B 470 ARG cc_start: 0.7631 (ptp-170) cc_final: 0.7282 (ptp-170) outliers start: 20 outliers final: 12 residues processed: 94 average time/residue: 0.2052 time to fit residues: 25.3161 Evaluate side-chains 91 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 0.0270 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5276 Z= 0.147 Angle : 0.572 11.188 7183 Z= 0.286 Chirality : 0.050 0.602 782 Planarity : 0.004 0.044 929 Dihedral : 7.055 55.930 853 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.14 % Allowed : 20.77 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.56 (0.33), residues: 645 helix: -0.82 (0.62), residues: 63 sheet: -1.46 (0.44), residues: 141 loop : -0.91 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 269 HIS 0.002 0.001 HIS A 465 PHE 0.018 0.001 PHE B 311 TYR 0.013 0.001 TYR A 426 ARG 0.003 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASN cc_start: 0.8507 (m-40) cc_final: 0.8236 (m-40) REVERT: A 536 LYS cc_start: 0.8864 (mmpt) cc_final: 0.8503 (mmpt) REVERT: B 157 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7416 (mt) REVERT: B 293 THR cc_start: 0.8601 (t) cc_final: 0.8373 (t) REVERT: B 458 ASP cc_start: 0.8618 (t0) cc_final: 0.8381 (t0) REVERT: B 463 SER cc_start: 0.8837 (t) cc_final: 0.8570 (p) outliers start: 18 outliers final: 10 residues processed: 90 average time/residue: 0.1694 time to fit residues: 19.9768 Evaluate side-chains 87 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5276 Z= 0.193 Angle : 0.599 11.396 7183 Z= 0.298 Chirality : 0.051 0.606 782 Planarity : 0.004 0.042 929 Dihedral : 7.043 56.770 847 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.97 % Allowed : 20.94 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.53 (0.32), residues: 645 helix: -0.78 (0.63), residues: 63 sheet: -1.26 (0.41), residues: 153 loop : -0.95 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 269 HIS 0.003 0.001 HIS B 169 PHE 0.011 0.001 PHE B 209 TYR 0.014 0.001 TYR A 426 ARG 0.003 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 ASN cc_start: 0.8505 (m-40) cc_final: 0.8268 (m-40) REVERT: A 447 ARG cc_start: 0.8706 (ptm160) cc_final: 0.8337 (ptt180) REVERT: A 536 LYS cc_start: 0.8872 (mmpt) cc_final: 0.8498 (mmpt) REVERT: B 157 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7458 (mt) REVERT: B 293 THR cc_start: 0.8609 (t) cc_final: 0.8382 (t) REVERT: B 458 ASP cc_start: 0.8610 (t0) cc_final: 0.8382 (t0) REVERT: B 463 SER cc_start: 0.8836 (t) cc_final: 0.8405 (p) REVERT: B 470 ARG cc_start: 0.7695 (ptp-170) cc_final: 0.7461 (ptp-170) outliers start: 17 outliers final: 14 residues processed: 86 average time/residue: 0.1660 time to fit residues: 18.6453 Evaluate side-chains 86 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5276 Z= 0.194 Angle : 0.607 11.424 7183 Z= 0.304 Chirality : 0.051 0.605 782 Planarity : 0.004 0.041 929 Dihedral : 7.130 58.578 847 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.14 % Allowed : 20.59 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.50 (0.32), residues: 645 helix: -0.78 (0.63), residues: 63 sheet: -1.15 (0.44), residues: 141 loop : -0.98 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 384 HIS 0.003 0.001 HIS B 169 PHE 0.011 0.001 PHE B 209 TYR 0.015 0.001 TYR A 426 ARG 0.003 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 413 ASN cc_start: 0.8495 (m-40) cc_final: 0.8240 (m-40) REVERT: A 536 LYS cc_start: 0.8877 (mmpt) cc_final: 0.8507 (mmpt) REVERT: A 553 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: B 157 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7510 (mt) REVERT: B 293 THR cc_start: 0.8597 (t) cc_final: 0.8391 (t) REVERT: B 463 SER cc_start: 0.8861 (t) cc_final: 0.8426 (p) REVERT: B 470 ARG cc_start: 0.7709 (ptp-170) cc_final: 0.7466 (ptp-170) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 0.1750 time to fit residues: 19.9959 Evaluate side-chains 91 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.0570 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 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 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5276 Z= 0.192 Angle : 0.630 11.411 7183 Z= 0.313 Chirality : 0.051 0.600 782 Planarity : 0.004 0.041 929 Dihedral : 7.070 56.191 847 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.97 % Allowed : 20.94 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.46 (0.32), residues: 645 helix: -0.72 (0.64), residues: 64 sheet: -1.12 (0.44), residues: 141 loop : -0.96 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 332 HIS 0.002 0.001 HIS B 169 PHE 0.010 0.001 PHE B 209 TYR 0.017 0.002 TYR A 528 ARG 0.003 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 413 ASN cc_start: 0.8484 (m-40) cc_final: 0.8241 (m-40) REVERT: A 536 LYS cc_start: 0.8871 (mmpt) cc_final: 0.8498 (mmpt) REVERT: A 553 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: B 157 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7521 (mt) REVERT: B 270 GLN cc_start: 0.8927 (tp40) cc_final: 0.8034 (tp40) REVERT: B 293 THR cc_start: 0.8570 (t) cc_final: 0.8363 (t) REVERT: B 463 SER cc_start: 0.8879 (t) cc_final: 0.8425 (p) REVERT: B 470 ARG cc_start: 0.7701 (ptp-170) cc_final: 0.7447 (ptp-170) outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 0.1743 time to fit residues: 19.3800 Evaluate side-chains 87 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 0.0470 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5276 Z= 0.202 Angle : 0.633 11.444 7183 Z= 0.318 Chirality : 0.052 0.601 782 Planarity : 0.004 0.041 929 Dihedral : 7.151 56.081 847 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.32 % Allowed : 20.59 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.44 (0.32), residues: 645 helix: -0.70 (0.64), residues: 64 sheet: -1.01 (0.43), residues: 139 loop : -0.99 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 269 HIS 0.003 0.001 HIS B 169 PHE 0.015 0.001 PHE B 311 TYR 0.017 0.002 TYR A 528 ARG 0.003 0.000 ARG B 470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 397 ARG cc_start: 0.8581 (mmm160) cc_final: 0.7883 (mmm160) REVERT: A 413 ASN cc_start: 0.8490 (m-40) cc_final: 0.8225 (m-40) REVERT: A 536 LYS cc_start: 0.8869 (mmpt) cc_final: 0.8500 (mmpt) REVERT: A 553 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: B 157 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7527 (mt) REVERT: B 270 GLN cc_start: 0.8900 (tp40) cc_final: 0.8037 (tp40) REVERT: B 463 SER cc_start: 0.8883 (t) cc_final: 0.8589 (p) outliers start: 19 outliers final: 16 residues processed: 86 average time/residue: 0.1772 time to fit residues: 19.7090 Evaluate side-chains 89 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 0.0070 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.074775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.064048 restraints weight = 13037.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.065467 restraints weight = 8785.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.066229 restraints weight = 5888.735| |-----------------------------------------------------------------------------| r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5276 Z= 0.176 Angle : 0.620 11.348 7183 Z= 0.308 Chirality : 0.051 0.590 782 Planarity : 0.004 0.041 929 Dihedral : 6.894 56.132 847 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.32 % Allowed : 20.42 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.41 (0.32), residues: 645 helix: -0.70 (0.64), residues: 64 sheet: -0.96 (0.44), residues: 139 loop : -0.97 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 269 HIS 0.003 0.001 HIS B 274 PHE 0.010 0.001 PHE B 311 TYR 0.017 0.001 TYR A 528 ARG 0.003 0.000 ARG B 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1490.76 seconds wall clock time: 27 minutes 39.29 seconds (1659.29 seconds total)