Starting phenix.real_space_refine on Thu Feb 13 12:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m4r_23665/02_2025/7m4r_23665.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m4r_23665/02_2025/7m4r_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/cci-nas-00/data/ceres_data/7m4r_23665/02_2025/7m4r_23665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m4r_23665/02_2025/7m4r_23665.map" model { file = "/net/cci-nas-00/data/ceres_data/7m4r_23665/02_2025/7m4r_23665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m4r_23665/02_2025/7m4r_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-5592/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: 3.40, per 1000 atoms: 0.67 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: 1.14 Conformation dependent library (CDL) restraints added in 619.2 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: 0.65 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: 1.21 Time building geometry restraints manager: 1.35 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: 1.400 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 15.230 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2405 time to fit residues: 14.3814 Evaluate side-chains 35 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.075042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.052402 restraints weight = 18127.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.054245 restraints weight = 10619.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.055432 restraints weight = 7726.265| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 275 MET cc_start: 0.9126 (tmm) cc_final: 0.8839 (tmm) REVERT: A 469 MET cc_start: 0.8859 (mmt) cc_final: 0.8483 (mmm) REVERT: A 550 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7544 (tm-30) REVERT: B 469 MET cc_start: 0.9376 (mmm) cc_final: 0.9069 (mmm) REVERT: B 528 TYR cc_start: 0.8640 (m-80) cc_final: 0.8152 (m-80) REVERT: B 529 HIS cc_start: 0.7659 (t-90) cc_final: 0.7026 (t-90) REVERT: B 547 GLU cc_start: 0.9044 (pp20) cc_final: 0.8743 (pp20) REVERT: B 605 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9133 (mt) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.2233 time to fit residues: 12.6431 Evaluate side-chains 39 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 605 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 62 optimal weight: 0.0470 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.077618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.055157 restraints weight = 18017.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.057238 restraints weight = 9929.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.058644 restraints weight = 6941.292| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5194 Z= 0.149 Angle : 0.585 8.823 7034 Z= 0.296 Chirality : 0.042 0.157 774 Planarity : 0.004 0.039 927 Dihedral : 5.135 33.517 701 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.91 % Allowed : 7.66 % Favored : 91.42 % 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: -1.95 (0.34), residues: 627 helix: 0.56 (0.41), residues: 161 sheet: -0.94 (0.42), residues: 156 loop : -2.57 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 668 HIS 0.003 0.001 HIS B 380 PHE 0.007 0.001 PHE B 536 TYR 0.012 0.001 TYR A 652 ARG 0.003 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 48 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.9245 (tmm) cc_final: 0.8832 (ppp) REVERT: A 299 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7212 (t0) REVERT: A 469 MET cc_start: 0.8893 (mmt) cc_final: 0.8499 (mmm) REVERT: A 605 LEU cc_start: 0.9371 (tt) cc_final: 0.9039 (mt) REVERT: B 361 ASP cc_start: 0.8724 (m-30) cc_final: 0.8377 (p0) REVERT: B 469 MET cc_start: 0.9366 (mmm) cc_final: 0.9132 (mmm) REVERT: B 500 MET cc_start: 0.8781 (tmm) cc_final: 0.8456 (ptt) REVERT: B 528 TYR cc_start: 0.8633 (m-80) cc_final: 0.8043 (m-80) REVERT: B 529 HIS cc_start: 0.7741 (t-90) cc_final: 0.7420 (t70) REVERT: B 547 GLU cc_start: 0.9033 (pp20) cc_final: 0.8831 (pp20) REVERT: B 605 LEU cc_start: 0.9449 (tp) cc_final: 0.9069 (mt) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 0.2207 time to fit residues: 13.2245 Evaluate side-chains 45 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 581 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.052869 restraints weight = 18761.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.054852 restraints weight = 10470.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.056190 restraints weight = 7405.709| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5194 Z= 0.240 Angle : 0.577 8.518 7034 Z= 0.293 Chirality : 0.042 0.158 774 Planarity : 0.004 0.036 927 Dihedral : 5.082 28.862 701 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 1.09 % Allowed : 9.67 % Favored : 89.23 % 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: -1.76 (0.35), residues: 627 helix: 0.87 (0.42), residues: 159 sheet: -0.71 (0.46), residues: 146 loop : -2.56 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 389 HIS 0.004 0.001 HIS A 637 PHE 0.008 0.001 PHE B 639 TYR 0.012 0.001 TYR B 363 ARG 0.002 0.000 ARG C 69 *********************** 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 41 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.9279 (tmm) cc_final: 0.8912 (ppp) REVERT: A 469 MET cc_start: 0.8908 (mmt) cc_final: 0.8549 (mmm) REVERT: B 469 MET cc_start: 0.9335 (mmm) cc_final: 0.9058 (mmm) REVERT: B 528 TYR cc_start: 0.8592 (m-80) cc_final: 0.8082 (m-80) REVERT: B 529 HIS cc_start: 0.7694 (t-90) cc_final: 0.7250 (t70) REVERT: B 605 LEU cc_start: 0.9461 (tp) cc_final: 0.9088 (mt) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.2500 time to fit residues: 12.7341 Evaluate side-chains 36 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 669 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.075547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.053191 restraints weight = 18336.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.055184 restraints weight = 10191.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056538 restraints weight = 7167.410| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2403 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= 0.214 Angle : 0.590 8.541 7034 Z= 0.296 Chirality : 0.042 0.150 774 Planarity : 0.004 0.034 927 Dihedral : 4.927 25.905 701 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 1.09 % Allowed : 11.31 % Favored : 87.59 % 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: -1.63 (0.35), residues: 627 helix: 1.01 (0.41), residues: 159 sheet: -0.69 (0.45), residues: 148 loop : -2.47 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 389 HIS 0.003 0.001 HIS B 380 PHE 0.006 0.001 PHE A 330 TYR 0.008 0.001 TYR B 393 ARG 0.002 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 39 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.9318 (tmm) cc_final: 0.8940 (ppp) REVERT: A 469 MET cc_start: 0.8948 (mmt) cc_final: 0.8518 (mmm) REVERT: B 469 MET cc_start: 0.9308 (mmm) cc_final: 0.9042 (mmm) REVERT: B 500 MET cc_start: 0.8750 (tmm) cc_final: 0.8462 (ptt) REVERT: B 528 TYR cc_start: 0.8633 (m-80) cc_final: 0.8137 (m-80) REVERT: B 529 HIS cc_start: 0.7723 (t-90) cc_final: 0.7066 (t-90) REVERT: B 605 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9066 (mt) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.2236 time to fit residues: 11.1337 Evaluate side-chains 34 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 605 LEU Chi-restraints excluded: chain B residue 637 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 54 optimal weight: 0.0980 chunk 47 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.074872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.052529 restraints weight = 18330.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.054479 restraints weight = 10303.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.055811 restraints weight = 7300.869| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5194 Z= 0.239 Angle : 0.584 8.415 7034 Z= 0.293 Chirality : 0.042 0.150 774 Planarity : 0.004 0.035 927 Dihedral : 4.904 23.929 701 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 1.46 % Allowed : 11.68 % 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: -1.58 (0.35), residues: 627 helix: 1.09 (0.41), residues: 160 sheet: -0.69 (0.45), residues: 148 loop : -2.46 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 389 HIS 0.004 0.001 HIS A 637 PHE 0.007 0.001 PHE B 639 TYR 0.009 0.001 TYR A 466 ARG 0.003 0.000 ARG B 675 *********************** 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 37 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.9364 (tmm) cc_final: 0.9072 (ppp) REVERT: A 469 MET cc_start: 0.8940 (mmt) cc_final: 0.8492 (mmm) REVERT: B 469 MET cc_start: 0.9284 (mmm) cc_final: 0.9028 (mmm) REVERT: B 528 TYR cc_start: 0.8654 (m-80) cc_final: 0.8182 (m-80) REVERT: B 529 HIS cc_start: 0.7790 (t-90) cc_final: 0.7083 (t-90) REVERT: B 605 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9086 (mt) outliers start: 8 outliers final: 6 residues processed: 36 average time/residue: 0.2379 time to fit residues: 11.1186 Evaluate side-chains 35 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 605 LEU Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 669 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 0.0010 chunk 52 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 overall best weight: 2.9792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.074252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.051955 restraints weight = 18508.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.053910 restraints weight = 10426.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.055206 restraints weight = 7376.609| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5194 Z= 0.263 Angle : 0.606 8.358 7034 Z= 0.304 Chirality : 0.042 0.142 774 Planarity : 0.004 0.036 927 Dihedral : 4.953 23.747 701 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 1.46 % Allowed : 12.23 % Favored : 86.31 % 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: -1.53 (0.35), residues: 627 helix: 1.14 (0.41), residues: 161 sheet: -0.72 (0.45), residues: 148 loop : -2.42 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 389 HIS 0.005 0.001 HIS B 380 PHE 0.007 0.001 PHE B 639 TYR 0.011 0.001 TYR A 466 ARG 0.003 0.000 ARG B 675 *********************** 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 38 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.9368 (tmm) cc_final: 0.9127 (ppp) REVERT: A 469 MET cc_start: 0.8954 (mmt) cc_final: 0.8491 (mmm) REVERT: B 469 MET cc_start: 0.9271 (mmm) cc_final: 0.9028 (mmm) REVERT: B 500 MET cc_start: 0.8731 (tmm) cc_final: 0.8457 (ptt) REVERT: B 528 TYR cc_start: 0.8638 (m-80) cc_final: 0.8122 (m-80) REVERT: B 529 HIS cc_start: 0.7842 (t-90) cc_final: 0.7068 (t-90) REVERT: B 605 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9115 (mt) REVERT: B 627 LYS cc_start: 0.9346 (mmmt) cc_final: 0.9125 (mmmt) outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 0.2316 time to fit residues: 11.1849 Evaluate side-chains 36 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 605 LEU Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 669 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.074912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.053231 restraints weight = 18118.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055106 restraints weight = 10399.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.056382 restraints weight = 7461.136| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2800 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= 0.209 Angle : 0.586 8.196 7034 Z= 0.290 Chirality : 0.042 0.142 774 Planarity : 0.004 0.040 927 Dihedral : 4.780 23.616 701 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 1.64 % Allowed : 12.59 % Favored : 85.77 % 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: -1.40 (0.35), residues: 627 helix: 1.29 (0.41), residues: 161 sheet: -0.66 (0.45), residues: 148 loop : -2.35 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 389 HIS 0.004 0.001 HIS B 380 PHE 0.006 0.001 PHE A 639 TYR 0.009 0.001 TYR B 363 ARG 0.003 0.000 ARG B 675 *********************** 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 40 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 MET cc_start: 0.8952 (mmt) cc_final: 0.8514 (mmm) REVERT: B 469 MET cc_start: 0.9245 (mmm) cc_final: 0.9020 (mmm) REVERT: B 528 TYR cc_start: 0.8675 (m-80) cc_final: 0.8126 (m-80) REVERT: B 529 HIS cc_start: 0.7864 (t-90) cc_final: 0.7201 (t70) REVERT: B 605 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9110 (mt) REVERT: B 627 LYS cc_start: 0.9336 (mmmt) cc_final: 0.9123 (mmmt) outliers start: 9 outliers final: 7 residues processed: 39 average time/residue: 0.2503 time to fit residues: 12.7316 Evaluate side-chains 37 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 605 LEU Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 669 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.052703 restraints weight = 18355.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.054654 restraints weight = 10434.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.055955 restraints weight = 7438.077| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2900 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= 0.198 Angle : 0.597 9.630 7034 Z= 0.295 Chirality : 0.042 0.145 774 Planarity : 0.004 0.037 927 Dihedral : 4.637 23.647 701 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 1.46 % Allowed : 12.77 % Favored : 85.77 % 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: -1.36 (0.35), residues: 627 helix: 1.33 (0.41), residues: 161 sheet: -0.75 (0.45), residues: 149 loop : -2.26 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 389 HIS 0.003 0.001 HIS B 380 PHE 0.006 0.001 PHE A 330 TYR 0.008 0.001 TYR A 466 ARG 0.003 0.000 ARG B 675 *********************** 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 to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 MET cc_start: 0.8950 (mmt) cc_final: 0.8486 (mmm) REVERT: B 469 MET cc_start: 0.9274 (mmm) cc_final: 0.9012 (mmm) REVERT: B 528 TYR cc_start: 0.8612 (m-80) cc_final: 0.8110 (m-80) REVERT: B 529 HIS cc_start: 0.7809 (t-90) cc_final: 0.7164 (t70) REVERT: B 605 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9128 (mt) REVERT: B 627 LYS cc_start: 0.9328 (mmmt) cc_final: 0.9116 (mmmt) outliers start: 8 outliers final: 6 residues processed: 38 average time/residue: 0.2237 time to fit residues: 11.0583 Evaluate side-chains 38 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 605 LEU Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 669 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 52 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.074786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.052545 restraints weight = 18562.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.054559 restraints weight = 10384.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.055908 restraints weight = 7329.150| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2990 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= 0.207 Angle : 0.610 9.060 7034 Z= 0.297 Chirality : 0.042 0.143 774 Planarity : 0.004 0.035 927 Dihedral : 4.568 23.703 701 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 1.46 % Allowed : 12.96 % Favored : 85.58 % 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: -1.28 (0.35), residues: 627 helix: 1.42 (0.41), residues: 161 sheet: -0.76 (0.44), residues: 149 loop : -2.18 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 389 HIS 0.003 0.001 HIS A 637 PHE 0.006 0.001 PHE A 330 TYR 0.009 0.001 TYR B 363 ARG 0.003 0.000 ARG B 675 ********************** 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 40 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 MET cc_start: 0.8954 (mmt) cc_final: 0.8484 (mmm) REVERT: B 469 MET cc_start: 0.9266 (mmm) cc_final: 0.9009 (mmm) REVERT: B 528 TYR cc_start: 0.8617 (m-80) cc_final: 0.8115 (m-80) REVERT: B 529 HIS cc_start: 0.7892 (t-90) cc_final: 0.7233 (t70) REVERT: B 605 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9116 (mt) REVERT: B 627 LYS cc_start: 0.9319 (mmmt) cc_final: 0.9110 (mttt) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.2379 time to fit residues: 11.8741 Evaluate side-chains 38 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 605 LEU Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 669 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 0.0970 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.075444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.053273 restraints weight = 18473.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.055324 restraints weight = 10295.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.056677 restraints weight = 7236.049| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3067 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= 0.173 Angle : 0.586 8.898 7034 Z= 0.287 Chirality : 0.042 0.140 774 Planarity : 0.004 0.034 927 Dihedral : 4.418 23.421 701 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.28 % Allowed : 13.32 % 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: -1.18 (0.35), residues: 627 helix: 1.49 (0.41), residues: 161 sheet: -0.72 (0.44), residues: 149 loop : -2.10 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 389 HIS 0.003 0.001 HIS A 637 PHE 0.006 0.001 PHE A 330 TYR 0.007 0.001 TYR A 652 ARG 0.004 0.000 ARG B 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1783.21 seconds wall clock time: 32 minutes 30.82 seconds (1950.82 seconds total)