Starting phenix.real_space_refine on Tue Sep 24 02:38:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyn_60573/09_2024/8zyn_60573.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyn_60573/09_2024/8zyn_60573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyn_60573/09_2024/8zyn_60573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyn_60573/09_2024/8zyn_60573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyn_60573/09_2024/8zyn_60573.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyn_60573/09_2024/8zyn_60573.cif" } resolution = 3.27 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= 0.004 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4462 2.51 5 N 1066 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1658 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 5 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1662 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1662 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1658 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 5 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 5.03, per 1000 atoms: 0.76 Number of scatterers: 6640 At special positions: 0 Unit cell: (92.13, 92.13, 73.87, 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 32 16.00 O 1080 8.00 N 1066 7.00 C 4462 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: 1.61 Conformation dependent library (CDL) restraints added in 904.2 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 409 through 431 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.851A pdb=" N PHE A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 removed outlier: 4.329A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.576A pdb=" N LEU A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 524 " --> pdb=" O ILE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.645A pdb=" N ALA A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.645A pdb=" N TYR A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 576 Processing helix chain 'A' and resid 584 through 593 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 634 through 665 removed outlier: 3.802A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 431 Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 453 through 471 removed outlier: 4.045A pdb=" N PHE B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.931A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 506 removed outlier: 4.345A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 546 through 574 removed outlier: 3.679A pdb=" N LEU B 550 " --> pdb=" O GLY B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 594 Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 634 through 664 removed outlier: 3.822A pdb=" N GLN B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 432 removed outlier: 3.791A pdb=" N TRP C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 453 through 470 Processing helix chain 'C' and resid 488 through 496 removed outlier: 4.103A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 506 removed outlier: 4.012A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 537 removed outlier: 3.697A pdb=" N THR C 526 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 533 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 537 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 545 through 575 removed outlier: 3.679A pdb=" N GLU C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 Processing helix chain 'C' and resid 606 through 624 Processing helix chain 'C' and resid 634 through 665 removed outlier: 3.809A pdb=" N GLN C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 431 Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 453 through 470 Processing helix chain 'D' and resid 488 through 495 removed outlier: 4.174A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 504 removed outlier: 3.513A pdb=" N ASP D 501 " --> pdb=" O TRP D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 531 removed outlier: 3.745A pdb=" N LEU D 524 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 537 removed outlier: 3.533A pdb=" N ALA D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 545 through 576 Processing helix chain 'D' and resid 584 through 593 removed outlier: 3.549A pdb=" N ASN D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 624 Processing helix chain 'D' and resid 634 through 664 removed outlier: 4.500A pdb=" N GLN D 664 " --> pdb=" O SER D 660 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1377 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: 1.77 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1939 1.34 - 1.46: 1274 1.46 - 1.57: 3535 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 6800 Sorted by residual: bond pdb=" N PHE C 508 " pdb=" CA PHE C 508 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.07e+00 bond pdb=" N ASP C 509 " pdb=" CA ASP C 509 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.59e+00 bond pdb=" N LEU C 510 " pdb=" CA LEU C 510 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.39e+00 bond pdb=" C ASP C 509 " pdb=" O ASP C 509 " ideal model delta sigma weight residual 1.234 1.252 -0.018 1.19e-02 7.06e+03 2.23e+00 bond pdb=" CB ARG C 582 " pdb=" CG ARG C 582 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.49e+00 ... (remaining 6795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 9056 1.57 - 3.14: 118 3.14 - 4.71: 34 4.71 - 6.28: 14 6.28 - 7.85: 6 Bond angle restraints: 9228 Sorted by residual: angle pdb=" N PHE C 508 " pdb=" CA PHE C 508 " pdb=" C PHE C 508 " ideal model delta sigma weight residual 112.59 107.75 4.84 1.22e+00 6.72e-01 1.57e+01 angle pdb=" CA ARG C 582 " pdb=" CB ARG C 582 " pdb=" CG ARG C 582 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.79e+00 angle pdb=" CB ARG D 665 " pdb=" CG ARG D 665 " pdb=" CD ARG D 665 " ideal model delta sigma weight residual 111.30 118.48 -7.18 2.30e+00 1.89e-01 9.73e+00 angle pdb=" CB ARG C 582 " pdb=" CG ARG C 582 " pdb=" CD ARG C 582 " ideal model delta sigma weight residual 111.30 118.04 -6.74 2.30e+00 1.89e-01 8.59e+00 angle pdb=" CG ARG C 582 " pdb=" CD ARG C 582 " pdb=" NE ARG C 582 " ideal model delta sigma weight residual 112.00 118.24 -6.24 2.20e+00 2.07e-01 8.04e+00 ... (remaining 9223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 3255 14.51 - 29.01: 439 29.01 - 43.52: 153 43.52 - 58.03: 32 58.03 - 72.53: 5 Dihedral angle restraints: 3884 sinusoidal: 1460 harmonic: 2424 Sorted by residual: dihedral pdb=" CB MET A 645 " pdb=" CG MET A 645 " pdb=" SD MET A 645 " pdb=" CE MET A 645 " ideal model delta sinusoidal sigma weight residual 180.00 -120.73 -59.27 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS D 538 " pdb=" CG LYS D 538 " pdb=" CD LYS D 538 " pdb=" CE LYS D 538 " ideal model delta sinusoidal sigma weight residual 180.00 121.19 58.81 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU C 550 " pdb=" CA LEU C 550 " pdb=" CB LEU C 550 " pdb=" CG LEU C 550 " ideal model delta sinusoidal sigma weight residual -60.00 -118.67 58.67 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 723 0.032 - 0.064: 264 0.064 - 0.096: 85 0.096 - 0.129: 17 0.129 - 0.161: 3 Chirality restraints: 1092 Sorted by residual: chirality pdb=" CA THR B 425 " pdb=" N THR B 425 " pdb=" C THR B 425 " pdb=" CB THR B 425 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA PHE A 656 " pdb=" N PHE A 656 " pdb=" C PHE A 656 " pdb=" CB PHE A 656 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA PHE B 656 " pdb=" N PHE B 656 " pdb=" C PHE B 656 " pdb=" CB PHE B 656 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1089 not shown) Planarity restraints: 1088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 595 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO B 596 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 596 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 596 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 425 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO B 426 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 426 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 426 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 656 " -0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" C PHE B 656 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE B 656 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY B 657 " -0.006 2.00e-02 2.50e+03 ... (remaining 1085 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1627 2.79 - 3.31: 6515 3.31 - 3.84: 10995 3.84 - 4.37: 12103 4.37 - 4.90: 21322 Nonbonded interactions: 52562 Sorted by model distance: nonbonded pdb=" OD2 ASP A 466 " pdb=" NH1 ARG A 534 " model vdw 2.256 3.120 nonbonded pdb=" OH TYR C 420 " pdb=" OD1 ASP C 456 " model vdw 2.296 3.040 nonbonded pdb=" OE1 GLN D 576 " pdb=" NE2 HIS D 587 " model vdw 2.303 3.120 nonbonded pdb=" OD2 ASP C 466 " pdb=" NH2 ARG C 534 " model vdw 2.309 3.120 nonbonded pdb=" O LEU B 523 " pdb=" OG1 THR B 526 " model vdw 2.310 3.040 ... (remaining 52557 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 407 through 494 or (resid 495 and (name N or name CA or na \ me C or name O or name CB )) or resid 496 through 665)) selection = (chain 'C' and (resid 407 through 494 or (resid 495 and (name N or name CA or na \ me C or name O or name CB )) or resid 496 through 665)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.070 Find NCS groups from input model: 0.250 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.003 0.037 6800 Z= 0.179 Angle : 0.555 7.853 9228 Z= 0.283 Chirality : 0.037 0.161 1092 Planarity : 0.003 0.043 1088 Dihedral : 15.249 72.533 2316 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.86 % Allowed : 24.78 % Favored : 74.35 % 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: 1.18 (0.30), residues: 792 helix: 0.93 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.54 (0.61), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 568 HIS 0.004 0.001 HIS A 492 PHE 0.017 0.001 PHE C 656 TYR 0.013 0.001 TYR C 616 ARG 0.004 0.000 ARG B 665 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.720 Fit side-chains REVERT: B 591 ASP cc_start: 0.8543 (t0) cc_final: 0.8188 (t0) REVERT: B 596 PRO cc_start: 0.7915 (Cg_exo) cc_final: 0.7613 (Cg_endo) REVERT: C 461 ILE cc_start: 0.8507 (mm) cc_final: 0.8170 (mt) REVERT: C 462 MET cc_start: 0.8597 (mpp) cc_final: 0.7738 (mpp) REVERT: C 493 TYR cc_start: 0.7474 (t80) cc_final: 0.6855 (t80) REVERT: C 624 SER cc_start: 0.8265 (p) cc_final: 0.7798 (m) REVERT: D 582 ARG cc_start: 0.6070 (mmp80) cc_final: 0.5421 (mmp80) outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 0.2415 time to fit residues: 34.0332 Evaluate side-chains 109 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 ASN D 573 ASN D 576 GLN D 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 6800 Z= 0.463 Angle : 0.664 7.438 9228 Z= 0.350 Chirality : 0.045 0.192 1092 Planarity : 0.005 0.045 1088 Dihedral : 4.485 33.947 893 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.32 % Allowed : 22.62 % Favored : 73.05 % 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: 0.57 (0.30), residues: 792 helix: 0.58 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -0.14 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 585 HIS 0.005 0.001 HIS B 562 PHE 0.025 0.002 PHE B 656 TYR 0.021 0.002 TYR C 616 ARG 0.003 0.001 ARG C 531 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 0.657 Fit side-chains REVERT: B 552 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8180 (mp) REVERT: B 591 ASP cc_start: 0.8535 (t0) cc_final: 0.8109 (t0) REVERT: B 596 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7813 (Cg_endo) REVERT: C 461 ILE cc_start: 0.8536 (mm) cc_final: 0.8243 (mt) REVERT: C 462 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7900 (mpp) REVERT: C 493 TYR cc_start: 0.7627 (t80) cc_final: 0.6957 (t80) REVERT: D 417 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7539 (mp) outliers start: 30 outliers final: 17 residues processed: 138 average time/residue: 0.2141 time to fit residues: 37.7557 Evaluate side-chains 133 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 573 ASN Chi-restraints excluded: chain D residue 655 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN B 587 HIS D 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6800 Z= 0.181 Angle : 0.503 6.742 9228 Z= 0.267 Chirality : 0.038 0.171 1092 Planarity : 0.004 0.034 1088 Dihedral : 3.857 29.290 891 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.03 % Allowed : 23.78 % Favored : 73.20 % 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: 1.07 (0.30), residues: 792 helix: 0.91 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.09 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 568 HIS 0.004 0.001 HIS C 578 PHE 0.020 0.001 PHE B 656 TYR 0.014 0.001 TYR C 616 ARG 0.002 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.752 Fit side-chains REVERT: B 428 SER cc_start: 0.8911 (t) cc_final: 0.8360 (p) REVERT: B 534 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7957 (mtt180) REVERT: B 624 SER cc_start: 0.8403 (p) cc_final: 0.7952 (m) REVERT: C 461 ILE cc_start: 0.8525 (mm) cc_final: 0.8285 (mt) REVERT: C 462 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8198 (mpp) REVERT: C 493 TYR cc_start: 0.7556 (t80) cc_final: 0.7116 (t80) REVERT: C 624 SER cc_start: 0.8311 (p) cc_final: 0.7822 (m) outliers start: 21 outliers final: 9 residues processed: 129 average time/residue: 0.2353 time to fit residues: 38.0343 Evaluate side-chains 116 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 499 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.0040 chunk 76 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS ** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6800 Z= 0.157 Angle : 0.483 6.741 9228 Z= 0.254 Chirality : 0.037 0.159 1092 Planarity : 0.003 0.033 1088 Dihedral : 3.665 22.110 890 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.31 % Allowed : 22.19 % Favored : 74.50 % 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: 1.33 (0.31), residues: 792 helix: 1.07 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.31 (0.64), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 568 HIS 0.003 0.001 HIS A 492 PHE 0.018 0.001 PHE B 656 TYR 0.013 0.001 TYR C 616 ARG 0.004 0.000 ARG C 582 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.778 Fit side-chains REVERT: A 528 ARG cc_start: 0.8728 (mtt-85) cc_final: 0.8494 (mtt180) REVERT: B 428 SER cc_start: 0.8926 (t) cc_final: 0.8393 (p) REVERT: B 534 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7882 (mtt180) REVERT: B 624 SER cc_start: 0.8350 (p) cc_final: 0.7929 (m) REVERT: C 461 ILE cc_start: 0.8575 (mm) cc_final: 0.8352 (mt) REVERT: C 462 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8179 (mpp) REVERT: C 493 TYR cc_start: 0.7430 (t80) cc_final: 0.6984 (t80) REVERT: C 575 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6849 (tm-30) REVERT: C 624 SER cc_start: 0.8272 (p) cc_final: 0.7781 (m) REVERT: D 633 ASN cc_start: 0.8806 (t0) cc_final: 0.8332 (t0) outliers start: 23 outliers final: 13 residues processed: 131 average time/residue: 0.2314 time to fit residues: 38.6286 Evaluate side-chains 126 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 497 TRP Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 0.0060 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS ** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6800 Z= 0.240 Angle : 0.538 7.023 9228 Z= 0.281 Chirality : 0.039 0.172 1092 Planarity : 0.004 0.034 1088 Dihedral : 3.740 16.154 888 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.46 % Allowed : 22.91 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.31), residues: 792 helix: 0.96 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.12 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 568 HIS 0.004 0.001 HIS A 492 PHE 0.020 0.001 PHE B 656 TYR 0.017 0.002 TYR C 616 ARG 0.002 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.714 Fit side-chains REVERT: B 428 SER cc_start: 0.8965 (t) cc_final: 0.8402 (p) REVERT: B 534 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7854 (mtt180) REVERT: B 552 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8365 (mt) REVERT: C 461 ILE cc_start: 0.8574 (mm) cc_final: 0.8345 (mt) REVERT: C 462 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8123 (mpp) REVERT: C 493 TYR cc_start: 0.7439 (t80) cc_final: 0.6922 (t80) REVERT: C 624 SER cc_start: 0.8330 (p) cc_final: 0.7811 (m) REVERT: D 650 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7968 (tt) outliers start: 24 outliers final: 13 residues processed: 122 average time/residue: 0.1887 time to fit residues: 29.0906 Evaluate side-chains 123 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.0000 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS ** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6800 Z= 0.231 Angle : 0.531 6.901 9228 Z= 0.276 Chirality : 0.039 0.171 1092 Planarity : 0.004 0.034 1088 Dihedral : 3.726 16.155 888 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.75 % Allowed : 23.05 % Favored : 73.20 % 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: 1.11 (0.31), residues: 792 helix: 0.95 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.04 (0.61), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 568 HIS 0.004 0.001 HIS A 492 PHE 0.020 0.001 PHE B 656 TYR 0.016 0.002 TYR C 616 ARG 0.002 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.522 Fit side-chains REVERT: B 428 SER cc_start: 0.8966 (t) cc_final: 0.8398 (p) REVERT: B 552 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8373 (mt) REVERT: C 434 LYS cc_start: 0.6354 (mmtm) cc_final: 0.5859 (ptpt) REVERT: C 461 ILE cc_start: 0.8580 (mm) cc_final: 0.8343 (mt) REVERT: C 462 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8144 (mpp) REVERT: C 493 TYR cc_start: 0.7485 (t80) cc_final: 0.6960 (t80) REVERT: C 624 SER cc_start: 0.8326 (p) cc_final: 0.7802 (m) REVERT: D 650 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7945 (tt) outliers start: 26 outliers final: 17 residues processed: 124 average time/residue: 0.2409 time to fit residues: 38.2804 Evaluate side-chains 126 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 497 TRP Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS ** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6800 Z= 0.180 Angle : 0.521 6.745 9228 Z= 0.269 Chirality : 0.038 0.163 1092 Planarity : 0.004 0.031 1088 Dihedral : 3.652 15.877 888 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.31 % Allowed : 24.35 % Favored : 72.33 % 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: 1.26 (0.31), residues: 792 helix: 1.05 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.13 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 568 HIS 0.004 0.001 HIS A 492 PHE 0.019 0.001 PHE B 656 TYR 0.014 0.001 TYR C 616 ARG 0.003 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.729 Fit side-chains REVERT: B 428 SER cc_start: 0.8960 (t) cc_final: 0.8404 (p) REVERT: B 534 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7817 (mtt180) REVERT: B 552 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8383 (mt) REVERT: C 461 ILE cc_start: 0.8570 (mm) cc_final: 0.8353 (mt) REVERT: C 462 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8179 (mpp) REVERT: C 493 TYR cc_start: 0.7466 (t80) cc_final: 0.6956 (t80) REVERT: C 624 SER cc_start: 0.8330 (p) cc_final: 0.7794 (m) REVERT: D 650 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7915 (tt) outliers start: 23 outliers final: 15 residues processed: 122 average time/residue: 0.2401 time to fit residues: 36.6351 Evaluate side-chains 122 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 497 TRP Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.0670 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS ** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6800 Z= 0.212 Angle : 0.541 6.840 9228 Z= 0.279 Chirality : 0.039 0.166 1092 Planarity : 0.004 0.033 1088 Dihedral : 3.681 15.964 888 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.60 % Allowed : 24.06 % Favored : 72.33 % 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: 1.22 (0.31), residues: 792 helix: 1.01 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.16 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 568 HIS 0.004 0.001 HIS A 492 PHE 0.019 0.001 PHE B 656 TYR 0.016 0.001 TYR C 616 ARG 0.002 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.713 Fit side-chains REVERT: B 428 SER cc_start: 0.8967 (t) cc_final: 0.8403 (p) REVERT: B 534 ARG cc_start: 0.8155 (ttm170) cc_final: 0.7800 (mtt180) REVERT: B 552 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8395 (mt) REVERT: C 461 ILE cc_start: 0.8585 (mm) cc_final: 0.8366 (mt) REVERT: C 462 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8138 (mpp) REVERT: C 493 TYR cc_start: 0.7433 (t80) cc_final: 0.6890 (t80) REVERT: C 624 SER cc_start: 0.8333 (p) cc_final: 0.7794 (m) REVERT: D 650 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7929 (tt) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.2372 time to fit residues: 37.2061 Evaluate side-chains 128 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 497 TRP Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 0.0570 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS ** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6800 Z= 0.169 Angle : 0.524 7.092 9228 Z= 0.269 Chirality : 0.038 0.161 1092 Planarity : 0.003 0.029 1088 Dihedral : 3.570 15.631 888 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.03 % Allowed : 24.78 % Favored : 72.19 % 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 (0.31), residues: 792 helix: 1.11 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.29 (0.63), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 568 HIS 0.004 0.001 HIS A 492 PHE 0.017 0.001 PHE B 656 TYR 0.014 0.001 TYR C 616 ARG 0.007 0.000 ARG D 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.725 Fit side-chains REVERT: B 428 SER cc_start: 0.8936 (t) cc_final: 0.8392 (p) REVERT: B 534 ARG cc_start: 0.8130 (ttm170) cc_final: 0.7790 (mtt180) REVERT: B 624 SER cc_start: 0.8416 (p) cc_final: 0.7875 (m) REVERT: C 461 ILE cc_start: 0.8576 (mm) cc_final: 0.8363 (mt) REVERT: C 462 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8143 (mpp) REVERT: C 493 TYR cc_start: 0.7418 (t80) cc_final: 0.6895 (t80) REVERT: C 582 ARG cc_start: 0.6280 (mmp80) cc_final: 0.5882 (mmp80) REVERT: C 624 SER cc_start: 0.8309 (p) cc_final: 0.7789 (m) REVERT: D 541 ARG cc_start: 0.8040 (ptm160) cc_final: 0.7802 (ptm160) REVERT: D 545 TYR cc_start: 0.5798 (m-10) cc_final: 0.5319 (m-80) REVERT: D 550 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8223 (tt) outliers start: 21 outliers final: 18 residues processed: 121 average time/residue: 0.2352 time to fit residues: 35.7511 Evaluate side-chains 127 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 TRP Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 545 TYR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 573 ASN Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS ** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6800 Z= 0.193 Angle : 0.540 7.110 9228 Z= 0.276 Chirality : 0.038 0.162 1092 Planarity : 0.003 0.031 1088 Dihedral : 3.594 15.626 888 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.17 % Allowed : 24.78 % Favored : 72.05 % 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: 1.34 (0.31), residues: 792 helix: 1.09 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.25 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 568 HIS 0.004 0.001 HIS A 492 PHE 0.018 0.001 PHE B 656 TYR 0.015 0.001 TYR C 616 ARG 0.007 0.000 ARG D 534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.723 Fit side-chains REVERT: B 428 SER cc_start: 0.8970 (t) cc_final: 0.8420 (p) REVERT: B 534 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7774 (mtt180) REVERT: B 552 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8393 (mt) REVERT: C 461 ILE cc_start: 0.8577 (mm) cc_final: 0.8363 (mt) REVERT: C 462 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8140 (mpp) REVERT: C 493 TYR cc_start: 0.7443 (t80) cc_final: 0.6905 (t80) REVERT: C 575 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7056 (tm-30) REVERT: C 582 ARG cc_start: 0.6272 (mmp80) cc_final: 0.5905 (mmp80) REVERT: C 624 SER cc_start: 0.8329 (p) cc_final: 0.7793 (m) REVERT: D 541 ARG cc_start: 0.8049 (ptm160) cc_final: 0.7808 (ptm160) REVERT: D 545 TYR cc_start: 0.5884 (m-10) cc_final: 0.5375 (m-80) REVERT: D 550 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8226 (tt) outliers start: 22 outliers final: 18 residues processed: 121 average time/residue: 0.2419 time to fit residues: 36.9098 Evaluate side-chains 129 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 TRP Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 545 TYR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS B 578 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.186788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129724 restraints weight = 8132.221| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.05 r_work: 0.3314 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6800 Z= 0.189 Angle : 0.536 6.969 9228 Z= 0.274 Chirality : 0.038 0.165 1092 Planarity : 0.003 0.030 1088 Dihedral : 3.578 15.541 888 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.17 % Allowed : 24.78 % Favored : 72.05 % 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: 1.36 (0.31), residues: 792 helix: 1.10 (0.20), residues: 672 sheet: None (None), residues: 0 loop : 0.27 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 568 HIS 0.004 0.001 HIS A 492 PHE 0.018 0.001 PHE C 656 TYR 0.015 0.001 TYR C 616 ARG 0.007 0.000 ARG D 534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.48 seconds wall clock time: 36 minutes 48.39 seconds (2208.39 seconds total)