Starting phenix.real_space_refine on Tue Sep 24 22:52:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4r_23665/09_2024/7m4r_23665.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4r_23665/09_2024/7m4r_23665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4r_23665/09_2024/7m4r_23665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4r_23665/09_2024/7m4r_23665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4r_23665/09_2024/7m4r_23665.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4r_23665/09_2024/7m4r_23665.cif" } resolution = 3.65 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4930 atoms to isotropic. 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 14 5.16 5 C 3208 2.51 5 N 904 2.21 5 O 966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 5092 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2868 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 342} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2155 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 254} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 69 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Time building chain proxies: 3.58, per 1000 atoms: 0.70 Number of scatterers: 5092 At special positions: 0 Unit cell: (77.976, 90.288, 104.652, 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 14 16.00 O 966 8.00 N 904 7.00 C 3208 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 - 3.00 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 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 535.6 milliseconds 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 32.1% alpha, 12.4% 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 248 through 252 removed outlier: 4.357A pdb=" N GLU A 252 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 313 through 322 removed outlier: 4.077A pdb=" N VAL A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 491 through 503 removed outlier: 3.773A pdb=" N LEU A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.939A pdb=" N ASN A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 609 Processing helix chain 'A' and resid 621 through 633 removed outlier: 3.674A pdb=" N GLN A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 removed outlier: 5.238A pdb=" N GLN A 653 " --> pdb=" O ASP A 649 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.734A pdb=" N ASN B 400 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 502 Processing helix chain 'B' and resid 532 through 543 removed outlier: 4.390A pdb=" N ILE B 540 " --> pdb=" O PHE B 536 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 3.807A pdb=" N ARG B 564 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 569 " --> pdb=" O GLN B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 581 Processing helix chain 'B' and resid 582 through 588 Processing helix chain 'B' and resid 601 through 609 Processing helix chain 'B' and resid 621 through 631 Processing helix chain 'B' and resid 647 through 650 Processing helix chain 'B' and resid 651 through 662 removed outlier: 4.155A pdb=" N ARG B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 675 removed outlier: 4.112A pdb=" N ARG B 675 " --> pdb=" O SER B 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 671 through 675' Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 257 Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 283 removed outlier: 6.442A pdb=" N THR A 270 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 73 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AA5, first strand: chain 'A' and resid 350 through 351 removed outlier: 3.508A pdb=" N LYS A 351 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 467 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 379 through 383 removed outlier: 7.021A pdb=" N GLN A 391 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 469 through 472 Processing sheet with id=AA8, first strand: chain 'A' and resid 574 through 576 removed outlier: 7.426A pdb=" N ILE A 482 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 483 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE A 597 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 485 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ILE A 643 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 596 " --> pdb=" O ILE A 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 350 removed outlier: 3.599A pdb=" N VAL B 350 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN B 391 " --> pdb=" O ILE B 382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 483 through 485 removed outlier: 6.359A pdb=" N ILE B 483 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR B 641 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 596 " --> pdb=" O THR B 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 507 through 509 Processing sheet with id=AB4, first strand: chain 'B' and resid 548 through 551 141 hydrogen bonds defined for protein. 363 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: 1.24 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1737 1.34 - 1.46: 899 1.46 - 1.58: 2536 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 5194 Sorted by residual: bond pdb=" C ILE A 333 " pdb=" N PRO A 334 " ideal model delta sigma weight residual 1.330 1.314 0.016 1.25e-02 6.40e+03 1.72e+00 bond pdb=" CA ASP A 397 " pdb=" CB ASP A 397 " ideal model delta sigma weight residual 1.528 1.546 -0.018 1.39e-02 5.18e+03 1.66e+00 bond pdb=" N ASP A 276 " pdb=" CA ASP A 276 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.59e+00 bond pdb=" CB ILE A 567 " pdb=" CG2 ILE A 567 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.36e+00 bond pdb=" CB VAL A 381 " pdb=" CG2 VAL A 381 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.29e+00 ... (remaining 5189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 6747 1.88 - 3.76: 245 3.76 - 5.64: 34 5.64 - 7.53: 6 7.53 - 9.41: 2 Bond angle restraints: 7034 Sorted by residual: angle pdb=" N ASP A 276 " pdb=" CA ASP A 276 " pdb=" C ASP A 276 " ideal model delta sigma weight residual 110.80 120.21 -9.41 2.13e+00 2.20e-01 1.95e+01 angle pdb=" C THR A 465 " pdb=" N TYR A 466 " pdb=" CA TYR A 466 " ideal model delta sigma weight residual 122.19 130.72 -8.53 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CA ARG C 69 " pdb=" CB ARG C 69 " pdb=" CG ARG C 69 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" N MET A 275 " pdb=" CA MET A 275 " pdb=" C MET A 275 " ideal model delta sigma weight residual 110.24 115.52 -5.28 1.47e+00 4.63e-01 1.29e+01 angle pdb=" C GLN A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta sigma weight residual 127.00 134.38 -7.38 2.40e+00 1.74e-01 9.46e+00 ... (remaining 7029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 2812 17.35 - 34.70: 287 34.70 - 52.06: 55 52.06 - 69.41: 10 69.41 - 86.76: 5 Dihedral angle restraints: 3169 sinusoidal: 1309 harmonic: 1860 Sorted by residual: dihedral pdb=" CA ARG C 69 " pdb=" C ARG C 69 " pdb=" N VAL C 70 " pdb=" CA VAL C 70 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA GLU A 522 " pdb=" C GLU A 522 " pdb=" N VAL A 523 " pdb=" CA VAL A 523 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ASP A 649 " pdb=" C ASP A 649 " pdb=" N LYS A 650 " pdb=" CA LYS A 650 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 3166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 596 0.056 - 0.111: 150 0.111 - 0.166: 26 0.166 - 0.222: 1 0.222 - 0.277: 1 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA ASP A 276 " pdb=" N ASP A 276 " pdb=" C ASP A 276 " pdb=" CB ASP A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA VAL C 70 " pdb=" N VAL C 70 " pdb=" C VAL C 70 " pdb=" CB VAL C 70 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE B 594 " pdb=" N ILE B 594 " pdb=" C ILE B 594 " pdb=" CB ILE B 594 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 771 not shown) Planarity restraints: 927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 364 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 365 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 511 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 512 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 480 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 481 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " 0.022 5.00e-02 4.00e+02 ... (remaining 924 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1222 2.79 - 3.32: 4587 3.32 - 3.84: 7187 3.84 - 4.37: 7646 4.37 - 4.90: 13303 Nonbonded interactions: 33945 Sorted by model distance: nonbonded pdb=" NZ LYS A 583 " pdb=" OH TYR A 638 " model vdw 2.259 3.120 nonbonded pdb=" NZ LYS A 261 " pdb=" O LEU A 321 " model vdw 2.267 3.120 nonbonded pdb=" O ASP A 640 " pdb=" OG1 THR A 641 " model vdw 2.297 3.040 nonbonded pdb=" OD1 ASP A 355 " pdb=" N TYR A 356 " model vdw 2.307 3.120 nonbonded pdb=" OG SER A 470 " pdb=" OG SER A 671 " model vdw 2.325 3.040 ... (remaining 33940 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.090 Find NCS groups from input model: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 5194 Z= 0.431 Angle : 0.833 9.408 7034 Z= 0.472 Chirality : 0.050 0.277 774 Planarity : 0.005 0.048 927 Dihedral : 14.707 86.759 1963 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.19 % Favored : 85.65 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.94 (0.33), residues: 627 helix: -0.60 (0.41), residues: 154 sheet: -1.38 (0.45), residues: 132 loop : -2.96 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 668 HIS 0.006 0.002 HIS B 380 PHE 0.025 0.003 PHE B 551 TYR 0.016 0.002 TYR B 652 ARG 0.005 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2335 time to fit residues: 14.0660 Evaluate side-chains 35 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS B 529 HIS B 645 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5194 Z= 0.349 Angle : 0.715 9.169 7034 Z= 0.364 Chirality : 0.045 0.167 774 Planarity : 0.005 0.044 927 Dihedral : 6.226 40.865 701 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 0.73 % Allowed : 5.66 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.45 (0.33), residues: 627 helix: 0.12 (0.41), residues: 159 sheet: -1.18 (0.44), residues: 146 loop : -2.85 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 389 HIS 0.005 0.001 HIS A 637 PHE 0.016 0.002 PHE B 536 TYR 0.011 0.002 TYR B 393 ARG 0.003 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 629 ARG cc_start: 0.5419 (tpt90) cc_final: 0.5202 (tmt170) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.2188 time to fit residues: 12.3419 Evaluate side-chains 36 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 581 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5194 Z= 0.290 Angle : 0.658 9.252 7034 Z= 0.333 Chirality : 0.043 0.160 774 Planarity : 0.004 0.042 927 Dihedral : 5.809 38.654 701 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 1.09 % Allowed : 8.58 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.10 (0.34), residues: 627 helix: 0.63 (0.41), residues: 158 sheet: -0.99 (0.45), residues: 146 loop : -2.75 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 389 HIS 0.005 0.001 HIS B 380 PHE 0.009 0.001 PHE B 639 TYR 0.011 0.001 TYR B 528 ARG 0.002 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 0.2413 time to fit residues: 12.2554 Evaluate side-chains 33 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5194 Z= 0.367 Angle : 0.710 9.281 7034 Z= 0.358 Chirality : 0.044 0.162 774 Planarity : 0.005 0.043 927 Dihedral : 5.889 36.073 701 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 1.09 % Allowed : 10.58 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.01 (0.34), residues: 627 helix: 0.74 (0.41), residues: 158 sheet: -0.96 (0.46), residues: 146 loop : -2.69 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 389 HIS 0.013 0.002 HIS B 529 PHE 0.012 0.001 PHE B 639 TYR 0.011 0.001 TYR B 393 ARG 0.002 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 629 ARG cc_start: 0.5471 (tpt90) cc_final: 0.5214 (tmt170) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.2548 time to fit residues: 11.8892 Evaluate side-chains 31 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 0.0010 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 HIS ** B 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 5194 Z= 0.156 Angle : 0.609 8.937 7034 Z= 0.307 Chirality : 0.043 0.164 774 Planarity : 0.004 0.040 927 Dihedral : 5.218 30.772 701 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 1.28 % Allowed : 11.86 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.71 (0.35), residues: 627 helix: 0.91 (0.41), residues: 159 sheet: -0.81 (0.44), residues: 156 loop : -2.50 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 668 HIS 0.007 0.001 HIS B 513 PHE 0.006 0.001 PHE B 536 TYR 0.009 0.001 TYR A 652 ARG 0.006 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.2493 time to fit residues: 12.0003 Evaluate side-chains 32 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain C residue 69 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.0020 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 380 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5194 Z= 0.202 Angle : 0.603 8.497 7034 Z= 0.304 Chirality : 0.043 0.155 774 Planarity : 0.004 0.035 927 Dihedral : 5.039 26.829 701 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 1.82 % Allowed : 12.77 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.64 (0.35), residues: 627 helix: 1.09 (0.41), residues: 159 sheet: -0.70 (0.45), residues: 146 loop : -2.52 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 668 HIS 0.011 0.001 HIS B 529 PHE 0.006 0.001 PHE B 639 TYR 0.013 0.001 TYR A 249 ARG 0.006 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 37 average time/residue: 0.2506 time to fit residues: 11.7720 Evaluate side-chains 33 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 69 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5194 Z= 0.224 Angle : 0.633 8.553 7034 Z= 0.313 Chirality : 0.043 0.155 774 Planarity : 0.004 0.034 927 Dihedral : 4.967 23.716 701 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 2.01 % Allowed : 13.14 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.59 (0.35), residues: 627 helix: 1.17 (0.41), residues: 160 sheet: -0.71 (0.45), residues: 146 loop : -2.50 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 668 HIS 0.011 0.001 HIS B 529 PHE 0.006 0.001 PHE A 639 TYR 0.008 0.001 TYR B 393 ARG 0.005 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 28 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 38 average time/residue: 0.2478 time to fit residues: 11.9239 Evaluate side-chains 33 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 69 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 0.0020 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5194 Z= 0.198 Angle : 0.621 9.106 7034 Z= 0.309 Chirality : 0.043 0.152 774 Planarity : 0.004 0.033 927 Dihedral : 4.813 23.616 701 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 1.46 % Allowed : 13.87 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.54 (0.35), residues: 627 helix: 1.19 (0.42), residues: 160 sheet: -0.75 (0.44), residues: 148 loop : -2.42 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 668 HIS 0.011 0.001 HIS B 529 PHE 0.006 0.001 PHE A 330 TYR 0.013 0.001 TYR A 249 ARG 0.004 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.2599 time to fit residues: 11.5387 Evaluate side-chains 32 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 69 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5194 Z= 0.185 Angle : 0.632 9.751 7034 Z= 0.311 Chirality : 0.043 0.154 774 Planarity : 0.004 0.033 927 Dihedral : 4.686 23.563 701 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 1.82 % Allowed : 14.23 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.35), residues: 627 helix: 1.29 (0.42), residues: 160 sheet: -0.72 (0.44), residues: 148 loop : -2.31 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 668 HIS 0.012 0.001 HIS B 529 PHE 0.005 0.001 PHE A 639 TYR 0.012 0.001 TYR A 249 ARG 0.004 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 29 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 0.2386 time to fit residues: 11.5741 Evaluate side-chains 33 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 69 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.0000 chunk 57 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5194 Z= 0.186 Angle : 0.622 10.104 7034 Z= 0.308 Chirality : 0.043 0.152 774 Planarity : 0.004 0.034 927 Dihedral : 4.555 23.573 701 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 1.46 % Allowed : 15.15 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.34 (0.35), residues: 627 helix: 1.33 (0.42), residues: 160 sheet: -0.74 (0.44), residues: 148 loop : -2.23 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 668 HIS 0.012 0.001 HIS B 529 PHE 0.005 0.001 PHE B 639 TYR 0.013 0.001 TYR A 249 ARG 0.003 0.000 ARG C 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.2668 time to fit residues: 11.7054 Evaluate side-chains 30 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 69 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 0.3980 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.074570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.052669 restraints weight = 18278.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.054551 restraints weight = 10431.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.055803 restraints weight = 7478.288| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5194 Z= 0.274 Angle : 0.681 10.687 7034 Z= 0.335 Chirality : 0.044 0.156 774 Planarity : 0.004 0.035 927 Dihedral : 4.797 24.059 701 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 1.28 % Allowed : 15.69 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.37 (0.35), residues: 627 helix: 1.35 (0.42), residues: 159 sheet: -0.82 (0.44), residues: 148 loop : -2.22 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 389 HIS 0.012 0.002 HIS B 529 PHE 0.007 0.001 PHE A 639 TYR 0.012 0.001 TYR A 249 ARG 0.004 0.000 ARG C 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1170.25 seconds wall clock time: 21 minutes 36.65 seconds (1296.65 seconds total)