Starting phenix.real_space_refine on Sun Mar 10 19:44:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqv_25396/03_2024/7sqv_25396.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqv_25396/03_2024/7sqv_25396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqv_25396/03_2024/7sqv_25396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqv_25396/03_2024/7sqv_25396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqv_25396/03_2024/7sqv_25396.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqv_25396/03_2024/7sqv_25396.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 21 5.16 5 C 2814 2.51 5 N 776 2.21 5 O 860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 517": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4471 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4084 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 32, 'TRANS': 490} Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 180 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 153 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 3.02, per 1000 atoms: 0.68 Number of scatterers: 4471 At special positions: 0 Unit cell: (78.225, 78.225, 91.0975, 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 21 16.00 O 860 8.00 N 776 7.00 C 2814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 884.8 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 41.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.288A pdb=" N PHE A 86 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.571A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 removed outlier: 6.321A pdb=" N ASP A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.603A pdb=" N ALA A 231 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.253A pdb=" N LEU A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 375 through 381 removed outlier: 4.090A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.591A pdb=" N ALA A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.531A pdb=" N LYS A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 529 through 546 Processing helix chain 'A' and resid 561 through 575 Processing helix chain 'C' and resid 598 through 602 removed outlier: 3.582A pdb=" N GLY C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 611 removed outlier: 3.900A pdb=" N ILE C 610 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 611 " --> pdb=" O GLY C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 611' Processing helix chain 'B' and resid 48 through 53 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 91 removed outlier: 6.958A pdb=" N ASN A 115 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ARG A 178 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A 117 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA A 180 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY A 119 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 182 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 121 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 5.847A pdb=" N TYR A 478 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE A 560 " --> pdb=" O TYR A 478 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 480 " --> pdb=" O TYR A 558 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR A 558 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASN A 482 " --> pdb=" O MET A 556 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N MET A 556 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A 484 " --> pdb=" O TRP A 554 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP A 554 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 486 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE A 412 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER A 325 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 14.442A pdb=" N TYR A 327 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A 285 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA A 326 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA A 283 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU A 281 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLN A 278 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 268 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ARG A 280 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 266 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 282 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 234 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA5, first strand: chain 'A' and resid 305 through 306 194 hydrogen bonds defined for protein. 531 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: 1.17 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1509 1.34 - 1.46: 864 1.46 - 1.58: 2145 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 4559 Sorted by residual: bond pdb=" CB ASN A 296 " pdb=" CG ASN A 296 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CA VAL A 311 " pdb=" CB VAL A 311 " ideal model delta sigma weight residual 1.537 1.546 -0.009 1.29e-02 6.01e+03 4.97e-01 bond pdb=" CA ILE A 429 " pdb=" C ILE A 429 " ideal model delta sigma weight residual 1.523 1.529 -0.006 9.20e-03 1.18e+04 4.20e-01 bond pdb=" CA ASN A 296 " pdb=" CB ASN A 296 " ideal model delta sigma weight residual 1.530 1.537 -0.008 1.38e-02 5.25e+03 3.18e-01 bond pdb=" CA GLU A 443 " pdb=" C GLU A 443 " ideal model delta sigma weight residual 1.519 1.525 -0.006 1.01e-02 9.80e+03 3.00e-01 ... (remaining 4554 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.39: 182 107.39 - 114.04: 2527 114.04 - 120.69: 1825 120.69 - 127.34: 1621 127.34 - 133.99: 49 Bond angle restraints: 6204 Sorted by residual: angle pdb=" C MET A 428 " pdb=" N ILE A 429 " pdb=" CA ILE A 429 " ideal model delta sigma weight residual 120.33 122.22 -1.89 8.00e-01 1.56e+00 5.57e+00 angle pdb=" CA ASN A 296 " pdb=" CB ASN A 296 " pdb=" CG ASN A 296 " ideal model delta sigma weight residual 112.60 114.51 -1.91 1.00e+00 1.00e+00 3.67e+00 angle pdb=" C ILE A 429 " pdb=" CA ILE A 429 " pdb=" CB ILE A 429 " ideal model delta sigma weight residual 114.00 111.69 2.31 1.31e+00 5.83e-01 3.11e+00 angle pdb=" C ASN A 296 " pdb=" CA ASN A 296 " pdb=" CB ASN A 296 " ideal model delta sigma weight residual 110.17 111.69 -1.52 1.11e+00 8.12e-01 1.88e+00 angle pdb=" C ARG A 215 " pdb=" N LEU A 216 " pdb=" CA LEU A 216 " ideal model delta sigma weight residual 121.81 119.15 2.66 1.94e+00 2.66e-01 1.88e+00 ... (remaining 6199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 2350 16.31 - 32.61: 276 32.61 - 48.92: 76 48.92 - 65.22: 21 65.22 - 81.53: 9 Dihedral angle restraints: 2732 sinusoidal: 1077 harmonic: 1655 Sorted by residual: dihedral pdb=" CA ASP A 542 " pdb=" CB ASP A 542 " pdb=" CG ASP A 542 " pdb=" OD1 ASP A 542 " ideal model delta sinusoidal sigma weight residual -30.00 -84.42 54.42 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" N GLU A 570 " pdb=" CA GLU A 570 " pdb=" CB GLU A 570 " pdb=" CG GLU A 570 " ideal model delta sinusoidal sigma weight residual -180.00 -122.41 -57.59 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB MET B 46 " pdb=" CG MET B 46 " pdb=" SD MET B 46 " pdb=" CE MET B 46 " ideal model delta sinusoidal sigma weight residual -60.00 -117.39 57.39 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 2729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 432 0.026 - 0.052: 155 0.052 - 0.078: 53 0.078 - 0.105: 35 0.105 - 0.131: 20 Chirality restraints: 695 Sorted by residual: chirality pdb=" CA ILE A 484 " pdb=" N ILE A 484 " pdb=" C ILE A 484 " pdb=" CB ILE A 484 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL A 256 " pdb=" N VAL A 256 " pdb=" C VAL A 256 " pdb=" CB VAL A 256 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE A 87 " pdb=" N ILE A 87 " pdb=" C ILE A 87 " pdb=" CB ILE A 87 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 692 not shown) Planarity restraints: 817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 335 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO A 336 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 92 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO A 93 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 512 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 513 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " -0.017 5.00e-02 4.00e+02 ... (remaining 814 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1406 2.83 - 3.35: 3660 3.35 - 3.87: 6882 3.87 - 4.38: 7919 4.38 - 4.90: 13889 Nonbonded interactions: 33756 Sorted by model distance: nonbonded pdb=" O ARG A 525 " pdb=" NH2 ARG A 533 " model vdw 2.314 2.520 nonbonded pdb=" NE2 GLN A 137 " pdb=" OD1 ASN A 142 " model vdw 2.341 2.520 nonbonded pdb=" OD1 ASP A 250 " pdb=" N ASN A 254 " model vdw 2.429 2.520 nonbonded pdb=" O SER B 63 " pdb=" OG SER B 63 " model vdw 2.433 2.440 nonbonded pdb=" NZ LYS A 439 " pdb=" O VAL A 440 " model vdw 2.444 2.520 ... (remaining 33751 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 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: 0.010 Extract box with map and model: 21.990 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:11.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.001 0.029 4559 Z= 0.100 Angle : 0.380 4.867 6204 Z= 0.208 Chirality : 0.040 0.131 695 Planarity : 0.004 0.049 817 Dihedral : 16.078 81.526 1672 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.63 % Allowed : 18.79 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.36), residues: 565 helix: 2.23 (0.39), residues: 191 sheet: 1.75 (0.47), residues: 127 loop : 0.20 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 519 HIS 0.001 0.000 HIS A 538 PHE 0.004 0.001 PHE D 631 TYR 0.004 0.001 TYR A 292 ARG 0.004 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.506 Fit side-chains REVERT: A 539 GLU cc_start: 0.7696 (tt0) cc_final: 0.7397 (tp30) outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 1.4310 time to fit residues: 78.6290 Evaluate side-chains 49 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 544 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4559 Z= 0.254 Angle : 0.480 4.858 6204 Z= 0.265 Chirality : 0.043 0.135 695 Planarity : 0.005 0.049 817 Dihedral : 4.543 47.787 634 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.46 % Allowed : 17.75 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.36), residues: 565 helix: 2.32 (0.39), residues: 193 sheet: 1.24 (0.45), residues: 130 loop : 0.33 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 519 HIS 0.002 0.001 HIS A 488 PHE 0.006 0.001 PHE A 577 TYR 0.010 0.001 TYR A 455 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.569 Fit side-chains REVERT: A 172 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8163 (mppt) outliers start: 7 outliers final: 2 residues processed: 51 average time/residue: 1.4449 time to fit residues: 76.2959 Evaluate side-chains 48 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain C residue 592 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4559 Z= 0.232 Angle : 0.469 4.841 6204 Z= 0.258 Chirality : 0.043 0.136 695 Planarity : 0.005 0.049 817 Dihedral : 3.765 20.310 631 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.67 % Allowed : 16.70 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.35), residues: 565 helix: 2.32 (0.39), residues: 192 sheet: 0.83 (0.43), residues: 139 loop : 0.37 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 519 HIS 0.002 0.001 HIS A 488 PHE 0.007 0.001 PHE A 577 TYR 0.009 0.001 TYR A 455 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.569 Fit side-chains REVERT: A 172 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8177 (mppt) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 1.5765 time to fit residues: 79.9913 Evaluate side-chains 50 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain C residue 592 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4559 Z= 0.192 Angle : 0.453 5.409 6204 Z= 0.247 Chirality : 0.042 0.134 695 Planarity : 0.005 0.049 817 Dihedral : 3.640 18.109 630 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.88 % Allowed : 17.33 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.35), residues: 565 helix: 2.37 (0.39), residues: 192 sheet: 0.82 (0.43), residues: 139 loop : 0.37 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 519 HIS 0.002 0.001 HIS A 488 PHE 0.006 0.001 PHE A 577 TYR 0.008 0.001 TYR A 455 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.492 Fit side-chains REVERT: A 172 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8229 (mppt) outliers start: 9 outliers final: 4 residues processed: 51 average time/residue: 1.5462 time to fit residues: 81.5318 Evaluate side-chains 52 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain C residue 592 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 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 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4559 Z= 0.218 Angle : 0.465 4.698 6204 Z= 0.255 Chirality : 0.042 0.135 695 Planarity : 0.005 0.049 817 Dihedral : 3.695 18.542 630 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.92 % Allowed : 16.70 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.35), residues: 565 helix: 2.37 (0.39), residues: 192 sheet: 0.78 (0.43), residues: 139 loop : 0.31 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 519 HIS 0.002 0.001 HIS A 488 PHE 0.007 0.001 PHE A 577 TYR 0.008 0.001 TYR A 455 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.541 Fit side-chains REVERT: A 172 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8204 (mppt) outliers start: 14 outliers final: 8 residues processed: 55 average time/residue: 1.4252 time to fit residues: 81.5297 Evaluate side-chains 53 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain B residue 60 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4559 Z= 0.191 Angle : 0.458 6.075 6204 Z= 0.248 Chirality : 0.042 0.134 695 Planarity : 0.005 0.049 817 Dihedral : 3.650 18.456 630 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.71 % Allowed : 17.12 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.35), residues: 565 helix: 2.40 (0.39), residues: 192 sheet: 0.79 (0.43), residues: 139 loop : 0.33 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 519 HIS 0.002 0.001 HIS A 488 PHE 0.006 0.001 PHE A 577 TYR 0.008 0.001 TYR A 455 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.480 Fit side-chains REVERT: A 172 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8198 (mppt) REVERT: A 233 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7090 (p0) outliers start: 13 outliers final: 8 residues processed: 53 average time/residue: 1.4451 time to fit residues: 79.5322 Evaluate side-chains 54 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain B residue 60 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 0.0020 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.0370 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4559 Z= 0.141 Angle : 0.424 4.670 6204 Z= 0.229 Chirality : 0.041 0.133 695 Planarity : 0.004 0.048 817 Dihedral : 3.515 17.330 630 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.88 % Allowed : 17.75 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.35), residues: 565 helix: 2.46 (0.39), residues: 193 sheet: 0.94 (0.43), residues: 137 loop : 0.39 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 519 HIS 0.001 0.000 HIS A 488 PHE 0.006 0.001 PHE A 299 TYR 0.009 0.001 TYR A 287 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.496 Fit side-chains REVERT: A 172 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8147 (mppt) REVERT: A 233 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7060 (p0) outliers start: 9 outliers final: 3 residues processed: 50 average time/residue: 1.4147 time to fit residues: 73.3229 Evaluate side-chains 49 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain B residue 60 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 48 optimal weight: 0.0270 chunk 50 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4559 Z= 0.157 Angle : 0.445 7.359 6204 Z= 0.237 Chirality : 0.041 0.132 695 Planarity : 0.004 0.048 817 Dihedral : 3.519 16.770 630 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.09 % Allowed : 17.75 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.35), residues: 565 helix: 2.51 (0.39), residues: 192 sheet: 0.97 (0.43), residues: 137 loop : 0.39 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 519 HIS 0.002 0.000 HIS A 488 PHE 0.006 0.001 PHE A 577 TYR 0.008 0.001 TYR A 287 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.546 Fit side-chains REVERT: A 172 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8153 (mppt) REVERT: A 233 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7048 (p0) outliers start: 10 outliers final: 4 residues processed: 51 average time/residue: 1.4471 time to fit residues: 76.5213 Evaluate side-chains 50 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain B residue 60 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.0870 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 0.0870 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4559 Z= 0.123 Angle : 0.404 4.620 6204 Z= 0.218 Chirality : 0.041 0.130 695 Planarity : 0.004 0.047 817 Dihedral : 3.367 15.553 630 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.04 % Allowed : 18.58 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.36), residues: 565 helix: 2.57 (0.39), residues: 193 sheet: 1.05 (0.44), residues: 137 loop : 0.45 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 519 HIS 0.001 0.000 HIS A 491 PHE 0.004 0.001 PHE A 157 TYR 0.008 0.001 TYR A 287 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.569 Fit side-chains REVERT: A 172 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8161 (mppt) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 1.5325 time to fit residues: 77.7571 Evaluate side-chains 49 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain B residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4559 Z= 0.224 Angle : 0.494 8.276 6204 Z= 0.264 Chirality : 0.042 0.134 695 Planarity : 0.005 0.049 817 Dihedral : 3.584 16.816 630 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.25 % Allowed : 19.00 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.35), residues: 565 helix: 2.50 (0.39), residues: 192 sheet: 0.86 (0.43), residues: 139 loop : 0.36 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 519 HIS 0.004 0.001 HIS A 538 PHE 0.007 0.001 PHE A 577 TYR 0.009 0.001 TYR A 455 ARG 0.001 0.000 ARG A 543 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.534 Fit side-chains REVERT: A 172 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8195 (mppt) REVERT: A 233 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6988 (p0) outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 1.5148 time to fit residues: 76.8420 Evaluate side-chains 49 residues out of total 479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain B residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 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 = 0.3154 r_free = 0.3154 target = 0.084711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.062807 restraints weight = 7262.730| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.82 r_work: 0.2615 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4559 Z= 0.204 Angle : 0.447 4.718 6204 Z= 0.244 Chirality : 0.042 0.135 695 Planarity : 0.005 0.048 817 Dihedral : 3.601 17.716 630 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.67 % Allowed : 18.79 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.35), residues: 565 helix: 2.47 (0.39), residues: 192 sheet: 0.85 (0.43), residues: 139 loop : 0.32 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 519 HIS 0.002 0.001 HIS A 488 PHE 0.007 0.001 PHE A 577 TYR 0.008 0.001 TYR A 455 ARG 0.001 0.000 ARG A 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.68 seconds wall clock time: 43 minutes 47.21 seconds (2627.21 seconds total)