Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:34:16 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/12_2021/7l7q_23216.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/12_2021/7l7q_23216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/12_2021/7l7q_23216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/12_2021/7l7q_23216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/12_2021/7l7q_23216.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/12_2021/7l7q_23216.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 5619 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1113 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "I" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3480 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 411} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Time building chain proxies: 3.32, per 1000 atoms: 0.59 Number of scatterers: 5619 At special positions: 0 Unit cell: (103.125, 87.45, 88.275, 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 27 16.00 O 1042 8.00 N 951 7.00 C 3599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 800.2 milliseconds 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 72.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'H' and resid 3 through 39 removed outlier: 4.119A pdb=" N LEU H 35 " --> pdb=" O ASP H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 72 removed outlier: 3.616A pdb=" N LEU H 53 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 89 removed outlier: 3.580A pdb=" N GLN H 87 " --> pdb=" O PHE H 83 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN H 88 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 96 removed outlier: 4.369A pdb=" N ASN H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 96' Processing helix chain 'H' and resid 96 through 109 removed outlier: 3.513A pdb=" N LEU H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU H 101 " --> pdb=" O ASP H 97 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN H 107 " --> pdb=" O SER H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 134 removed outlier: 3.847A pdb=" N LYS H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 302 Processing helix chain 'I' and resid 311 through 317 removed outlier: 3.536A pdb=" N LYS I 317 " --> pdb=" O ASP I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 348 removed outlier: 4.241A pdb=" N SER I 341 " --> pdb=" O LYS I 337 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER I 342 " --> pdb=" O HIS I 338 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU I 345 " --> pdb=" O SER I 341 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE I 346 " --> pdb=" O SER I 342 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN I 348 " --> pdb=" O ILE I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 369 Processing helix chain 'I' and resid 374 through 388 removed outlier: 4.135A pdb=" N VAL I 378 " --> pdb=" O THR I 374 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE I 379 " --> pdb=" O PRO I 375 " (cutoff:3.500A) Proline residue: I 380 - end of helix removed outlier: 3.576A pdb=" N MET I 388 " --> pdb=" O SER I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 401 removed outlier: 3.637A pdb=" N ARG I 395 " --> pdb=" O LYS I 391 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 421 removed outlier: 3.674A pdb=" N LEU I 413 " --> pdb=" O ASP I 409 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS I 414 " --> pdb=" O GLU I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 431 No H-bonds generated for 'chain 'I' and resid 429 through 431' Processing helix chain 'I' and resid 432 through 448 Processing helix chain 'I' and resid 456 through 475 removed outlier: 3.712A pdb=" N THR I 461 " --> pdb=" O THR I 457 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP I 475 " --> pdb=" O ASN I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 removed outlier: 4.654A pdb=" N HIS I 487 " --> pdb=" O LEU I 483 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP I 488 " --> pdb=" O THR I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 506 through 525 removed outlier: 3.738A pdb=" N SER I 514 " --> pdb=" O MET I 510 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU I 519 " --> pdb=" O SER I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 538 through 547 removed outlier: 4.872A pdb=" N LYS I 544 " --> pdb=" O ASP I 540 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL I 545 " --> pdb=" O ILE I 541 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 563 Processing helix chain 'I' and resid 564 through 568 Processing helix chain 'I' and resid 577 through 589 removed outlier: 3.571A pdb=" N GLN I 583 " --> pdb=" O ARG I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 616 removed outlier: 3.526A pdb=" N LYS I 612 " --> pdb=" O PRO I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 640 through 654 removed outlier: 3.648A pdb=" N GLU I 654 " --> pdb=" O LEU I 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 666 through 676 removed outlier: 3.784A pdb=" N ASN I 671 " --> pdb=" O GLU I 667 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE I 673 " --> pdb=" O THR I 669 " (cutoff:3.500A) Processing helix chain 'I' and resid 677 through 684 removed outlier: 3.565A pdb=" N ILE I 681 " --> pdb=" O HIS I 677 " (cutoff:3.500A) Processing helix chain 'I' and resid 692 through 705 Processing helix chain 'I' and resid 709 through 711 No H-bonds generated for 'chain 'I' and resid 709 through 711' Processing helix chain 'I' and resid 712 through 723 removed outlier: 3.554A pdb=" N ALA I 716 " --> pdb=" O ARG I 712 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS I 723 " --> pdb=" O PHE I 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 40 Processing helix chain 'K' and resid 69 through 129 removed outlier: 4.354A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER K 80 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU K 88 " --> pdb=" O GLN K 84 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP K 99 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 951 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: 1.44 Time building geometry restraints manager: 2.54 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: 1790 1.34 - 1.45: 838 1.45 - 1.57: 3051 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 5725 Sorted by residual: bond pdb=" C ASP K 68 " pdb=" N PRO K 69 " ideal model delta sigma weight residual 1.334 1.317 0.016 8.40e-03 1.42e+04 3.76e+00 bond pdb=" CA GLU I 616 " pdb=" CB GLU I 616 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.66e-02 3.63e+03 2.44e+00 bond pdb=" N THR I 634 " pdb=" CA THR I 634 " ideal model delta sigma weight residual 1.464 1.443 0.020 1.30e-02 5.92e+03 2.44e+00 bond pdb=" CB CYS I 643 " pdb=" SG CYS I 643 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.29e+00 bond pdb=" CA PRO K 60 " pdb=" C PRO K 60 " ideal model delta sigma weight residual 1.525 1.512 0.014 9.70e-03 1.06e+04 2.04e+00 ... (remaining 5720 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 119 106.67 - 113.49: 3291 113.49 - 120.32: 2135 120.32 - 127.15: 2128 127.15 - 133.97: 55 Bond angle restraints: 7728 Sorted by residual: angle pdb=" C ASP I 549 " pdb=" N ASP I 550 " pdb=" CA ASP I 550 " ideal model delta sigma weight residual 120.67 108.05 12.62 1.34e+00 5.57e-01 8.87e+01 angle pdb=" N ALA I 708 " pdb=" CA ALA I 708 " pdb=" C ALA I 708 " ideal model delta sigma weight residual 114.75 106.21 8.54 1.26e+00 6.30e-01 4.59e+01 angle pdb=" N PRO I 318 " pdb=" CA PRO I 318 " pdb=" CB PRO I 318 " ideal model delta sigma weight residual 103.00 110.31 -7.31 1.10e+00 8.26e-01 4.42e+01 angle pdb=" N THR I 564 " pdb=" CA THR I 564 " pdb=" C THR I 564 " ideal model delta sigma weight residual 114.75 107.82 6.93 1.26e+00 6.30e-01 3.03e+01 angle pdb=" N GLY I 605 " pdb=" CA GLY I 605 " pdb=" C GLY I 605 " ideal model delta sigma weight residual 114.69 109.20 5.49 1.19e+00 7.06e-01 2.13e+01 ... (remaining 7723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 3063 17.58 - 35.16: 349 35.16 - 52.74: 70 52.74 - 70.32: 8 70.32 - 87.90: 9 Dihedral angle restraints: 3499 sinusoidal: 1454 harmonic: 2045 Sorted by residual: dihedral pdb=" CA GLY I 663 " pdb=" C GLY I 663 " pdb=" N ILE I 664 " pdb=" CA ILE I 664 " ideal model delta harmonic sigma weight residual 180.00 148.95 31.05 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA SER I 662 " pdb=" C SER I 662 " pdb=" N GLY I 663 " pdb=" CA GLY I 663 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE I 368 " pdb=" C PHE I 368 " pdb=" N ALA I 369 " pdb=" CA ALA I 369 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 3496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 659 0.049 - 0.098: 203 0.098 - 0.146: 20 0.146 - 0.195: 2 0.195 - 0.244: 2 Chirality restraints: 886 Sorted by residual: chirality pdb=" CA PRO I 318 " pdb=" N PRO I 318 " pdb=" C PRO I 318 " pdb=" CB PRO I 318 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB ILE I 665 " pdb=" CA ILE I 665 " pdb=" CG1 ILE I 665 " pdb=" CG2 ILE I 665 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE I 633 " pdb=" N ILE I 633 " pdb=" C ILE I 633 " pdb=" CB ILE I 633 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 883 not shown) Planarity restraints: 969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP H 97 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ASP H 97 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP H 97 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR H 98 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY I 538 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO I 539 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO I 539 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 539 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 421 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO I 422 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO I 422 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 422 " -0.015 5.00e-02 4.00e+02 ... (remaining 966 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 64 2.48 - 3.08: 4601 3.08 - 3.69: 9262 3.69 - 4.29: 12897 4.29 - 4.90: 19936 Nonbonded interactions: 46760 Sorted by model distance: nonbonded pdb=" OE1 GLU H 99 " pdb=" CD2 LEU K 90 " model vdw 1.873 3.460 nonbonded pdb=" O ILE I 382 " pdb=" OG SER I 386 " model vdw 2.092 2.440 nonbonded pdb=" CE1 TYR H 98 " pdb=" O ALA I 708 " model vdw 2.140 3.340 nonbonded pdb=" O PHE I 512 " pdb=" OG SER I 515 " model vdw 2.172 2.440 nonbonded pdb=" O PHE I 439 " pdb=" OG SER I 442 " model vdw 2.200 2.440 ... (remaining 46755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3599 2.51 5 N 951 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 Write .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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.050 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.040 Process input model: 18.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:1.970 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.005 0.050 5725 Z= 0.356 Angle : 0.911 12.619 7728 Z= 0.600 Chirality : 0.045 0.244 886 Planarity : 0.004 0.034 969 Dihedral : 15.540 87.901 2159 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.16 % Favored : 89.54 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.40 (0.25), residues: 679 helix: -2.55 (0.18), residues: 450 sheet: None (None), residues: 0 loop : -3.38 (0.35), residues: 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.2298 time to fit residues: 48.2957 Evaluate side-chains 112 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 0.0010 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 19 HIS H 94 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 GLN I 363 GLN I 370 HIS I 390 ASN I 525 GLN I 543 ASN I 671 ASN I 684 HIS I 703 HIS K 18 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5725 Z= 0.228 Angle : 0.764 8.822 7728 Z= 0.395 Chirality : 0.045 0.348 886 Planarity : 0.005 0.082 969 Dihedral : 5.780 28.059 735 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.39 % Favored : 91.46 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.31), residues: 679 helix: -0.77 (0.23), residues: 473 sheet: None (None), residues: 0 loop : -2.83 (0.42), residues: 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 172 average time/residue: 0.2146 time to fit residues: 46.7277 Evaluate side-chains 123 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0588 time to fit residues: 1.9937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 GLN I 525 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 5725 Z= 0.235 Angle : 0.771 13.425 7728 Z= 0.388 Chirality : 0.045 0.313 886 Planarity : 0.005 0.086 969 Dihedral : 5.564 27.978 735 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.84 % Favored : 91.02 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.32), residues: 679 helix: -0.17 (0.24), residues: 471 sheet: None (None), residues: 0 loop : -2.55 (0.45), residues: 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 156 average time/residue: 0.1865 time to fit residues: 37.3970 Evaluate side-chains 122 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0632 time to fit residues: 1.7885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 5725 Z= 0.242 Angle : 0.776 15.217 7728 Z= 0.390 Chirality : 0.046 0.280 886 Planarity : 0.005 0.088 969 Dihedral : 5.411 26.839 735 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.25 % Favored : 91.61 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.33), residues: 679 helix: 0.09 (0.23), residues: 475 sheet: None (None), residues: 0 loop : -2.41 (0.46), residues: 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 140 average time/residue: 0.1861 time to fit residues: 33.6188 Evaluate side-chains 123 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.609 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0565 time to fit residues: 1.8093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 671 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 5725 Z= 0.264 Angle : 0.795 10.947 7728 Z= 0.400 Chirality : 0.046 0.261 886 Planarity : 0.005 0.097 969 Dihedral : 5.401 28.442 735 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.33), residues: 679 helix: 0.18 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.36 (0.47), residues: 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 138 average time/residue: 0.1839 time to fit residues: 33.0484 Evaluate side-chains 115 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1797 time to fit residues: 1.8987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.0010 chunk 47 optimal weight: 0.4980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5725 Z= 0.222 Angle : 0.787 11.532 7728 Z= 0.393 Chirality : 0.045 0.259 886 Planarity : 0.004 0.075 969 Dihedral : 5.252 28.794 735 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.33), residues: 679 helix: 0.32 (0.24), residues: 476 sheet: None (None), residues: 0 loop : -2.16 (0.48), residues: 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 134 average time/residue: 0.1715 time to fit residues: 30.5480 Evaluate side-chains 117 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0630 time to fit residues: 1.5817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 ASN ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 5725 Z= 0.243 Angle : 0.813 11.993 7728 Z= 0.402 Chirality : 0.046 0.305 886 Planarity : 0.005 0.110 969 Dihedral : 5.137 25.453 735 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.34), residues: 679 helix: 0.45 (0.24), residues: 476 sheet: None (None), residues: 0 loop : -2.16 (0.48), residues: 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 130 average time/residue: 0.1875 time to fit residues: 32.2803 Evaluate side-chains 115 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0629 time to fit residues: 1.4715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.0170 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 0.0570 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN K 14 ASN K 18 GLN ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 5725 Z= 0.230 Angle : 0.840 12.279 7728 Z= 0.409 Chirality : 0.046 0.299 886 Planarity : 0.005 0.092 969 Dihedral : 5.145 33.453 735 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.34), residues: 679 helix: 0.54 (0.24), residues: 476 sheet: None (None), residues: 0 loop : -2.00 (0.49), residues: 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 130 average time/residue: 0.1684 time to fit residues: 29.0971 Evaluate side-chains 118 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0587 time to fit residues: 1.6367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 5725 Z= 0.245 Angle : 0.855 12.576 7728 Z= 0.418 Chirality : 0.045 0.285 886 Planarity : 0.006 0.124 969 Dihedral : 5.050 27.488 735 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.35), residues: 679 helix: 0.66 (0.24), residues: 474 sheet: None (None), residues: 0 loop : -1.88 (0.51), residues: 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 120 average time/residue: 0.1670 time to fit residues: 26.9490 Evaluate side-chains 113 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0574 time to fit residues: 1.1124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 HIS ** I 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 5725 Z= 0.302 Angle : 0.895 12.972 7728 Z= 0.437 Chirality : 0.049 0.442 886 Planarity : 0.005 0.102 969 Dihedral : 5.179 29.504 735 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.34), residues: 679 helix: 0.60 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -1.94 (0.50), residues: 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.663 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 0.1630 time to fit residues: 24.0001 Evaluate side-chains 104 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0712 time to fit residues: 1.0776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.078036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.065506 restraints weight = 24445.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.067666 restraints weight = 14135.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.069216 restraints weight = 9564.747| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 5725 Z= 0.251 Angle : 0.890 13.505 7728 Z= 0.426 Chirality : 0.048 0.355 886 Planarity : 0.005 0.092 969 Dihedral : 5.159 26.718 735 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.34), residues: 679 helix: 0.64 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -1.97 (0.51), residues: 204 =============================================================================== Job complete usr+sys time: 1485.13 seconds wall clock time: 27 minutes 46.50 seconds (1666.50 seconds total)