Starting phenix.real_space_refine on Mon Feb 10 22:08:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh4_14721/02_2025/7zh4_14721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh4_14721/02_2025/7zh4_14721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zh4_14721/02_2025/7zh4_14721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh4_14721/02_2025/7zh4_14721.map" model { file = "/net/cci-nas-00/data/ceres_data/7zh4_14721/02_2025/7zh4_14721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh4_14721/02_2025/7zh4_14721.cif" } resolution = 2.49 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= 0.000 sd= 0.180 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 13 5.16 5 C 1869 2.51 5 N 483 2.21 5 O 591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2957 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2281 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 6 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' ZN': 1, 'JDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1467 SG CYS D 440 35.067 73.958 21.289 1.00 8.28 S ATOM 1490 SG CYS D 443 36.874 74.553 18.050 1.00 9.34 S ATOM 1865 SG CYS D 506 38.863 73.268 20.965 1.00 7.56 S ATOM 1888 SG CYS D 509 37.602 76.874 20.899 1.00 8.94 S Time building chain proxies: 2.98, per 1000 atoms: 1.01 Number of scatterers: 2957 At special positions: 0 Unit cell: (64.66, 87.98, 58.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 13 16.00 O 591 8.00 N 483 7.00 C 1869 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: 0.87 Conformation dependent library (CDL) restraints added in 346.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 443 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 509 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 506 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 440 " Number of angles added : 6 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 686 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 7 sheets defined 40.3% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.579A pdb=" N TYR C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 88 Processing helix chain 'D' and resid 89 through 101 removed outlier: 3.671A pdb=" N PHE D 101 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 144 through 166 Processing helix chain 'D' and resid 200 through 220 Processing helix chain 'D' and resid 424 through 431 removed outlier: 3.584A pdb=" N GLN D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.705A pdb=" N LYS D 503 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 759 through 767 Processing helix chain 'D' and resid 768 through 772 Processing sheet with id=AA1, first strand: chain 'C' and resid 12 through 17 removed outlier: 8.944A pdb=" N LEU C 67 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 4 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU C 69 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS C 6 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'D' and resid 446 through 453 Processing sheet with id=AA4, first strand: chain 'D' and resid 456 through 459 removed outlier: 5.865A pdb=" N ILE D 456 " --> pdb=" O HIS D 531 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS D 533 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL D 458 " --> pdb=" O LYS D 533 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR D 778 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR D 782 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU D 578 " --> pdb=" O TYR D 782 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS D 784 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR D 576 " --> pdb=" O LYS D 784 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 456 through 459 removed outlier: 5.865A pdb=" N ILE D 456 " --> pdb=" O HIS D 531 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS D 533 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL D 458 " --> pdb=" O LYS D 533 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR D 778 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR D 782 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU D 578 " --> pdb=" O TYR D 782 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS D 784 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR D 576 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE D 579 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 596 " --> pdb=" O PHE D 750 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 504 through 506 Processing sheet with id=AA7, first strand: chain 'D' and resid 535 through 536 163 hydrogen bonds defined for protein. 423 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: 0.83 Time building geometry restraints manager: 0.91 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: 924 1.34 - 1.46: 574 1.46 - 1.58: 1452 1.58 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 2967 Sorted by residual: bond pdb=" C12 JDA D1001 " pdb=" C13 JDA D1001 " ideal model delta sigma weight residual 1.371 1.352 0.019 2.00e-02 2.50e+03 9.38e-01 bond pdb=" C16 JDA D1001 " pdb=" C17 JDA D1001 " ideal model delta sigma weight residual 1.392 1.373 0.019 2.00e-02 2.50e+03 9.26e-01 bond pdb=" CA GLY D 577 " pdb=" C GLY D 577 " ideal model delta sigma weight residual 1.512 1.519 -0.007 8.70e-03 1.32e+04 7.36e-01 bond pdb=" N JDA D1001 " pdb=" C2 JDA D1001 " ideal model delta sigma weight residual 1.348 1.332 0.016 2.00e-02 2.50e+03 6.44e-01 bond pdb=" CG ARG D 118 " pdb=" CD ARG D 118 " ideal model delta sigma weight residual 1.520 1.497 0.023 3.00e-02 1.11e+03 6.09e-01 ... (remaining 2962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 3835 1.37 - 2.74: 141 2.74 - 4.11: 19 4.11 - 5.48: 3 5.48 - 6.85: 3 Bond angle restraints: 4001 Sorted by residual: angle pdb=" C SER D 117 " pdb=" N ARG D 118 " pdb=" CA ARG D 118 " ideal model delta sigma weight residual 121.94 115.09 6.85 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CA ARG D 118 " pdb=" CB ARG D 118 " pdb=" CG ARG D 118 " ideal model delta sigma weight residual 114.10 118.69 -4.59 2.00e+00 2.50e-01 5.26e+00 angle pdb=" C LEU D 557 " pdb=" N THR D 558 " pdb=" CA THR D 558 " ideal model delta sigma weight residual 120.94 125.10 -4.16 1.90e+00 2.77e-01 4.79e+00 angle pdb=" CA LYS D 533 " pdb=" C LYS D 533 " pdb=" N CYS D 534 " ideal model delta sigma weight residual 114.76 117.04 -2.28 1.14e+00 7.69e-01 4.01e+00 angle pdb=" CA LYS D 533 " pdb=" C LYS D 533 " pdb=" O LYS D 533 " ideal model delta sigma weight residual 122.64 120.41 2.23 1.25e+00 6.40e-01 3.18e+00 ... (remaining 3996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 1617 15.83 - 31.67: 128 31.67 - 47.50: 42 47.50 - 63.34: 8 63.34 - 79.17: 5 Dihedral angle restraints: 1800 sinusoidal: 749 harmonic: 1051 Sorted by residual: dihedral pdb=" CA PHE D 492 " pdb=" C PHE D 492 " pdb=" N ALA D 493 " pdb=" CA ALA D 493 " ideal model delta harmonic sigma weight residual -180.00 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP D 463 " pdb=" CB ASP D 463 " pdb=" CG ASP D 463 " pdb=" OD1 ASP D 463 " ideal model delta sinusoidal sigma weight residual -30.00 -87.42 57.42 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CG LYS C 29 " pdb=" CD LYS C 29 " pdb=" CE LYS C 29 " pdb=" NZ LYS C 29 " ideal model delta sinusoidal sigma weight residual 60.00 116.94 -56.94 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 1797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 264 0.026 - 0.052: 122 0.052 - 0.078: 45 0.078 - 0.104: 18 0.104 - 0.130: 13 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA VAL D 755 " pdb=" N VAL D 755 " pdb=" C VAL D 755 " pdb=" CB VAL D 755 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE C 36 " pdb=" N ILE C 36 " pdb=" C ILE C 36 " pdb=" CB ILE C 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE D 456 " pdb=" N ILE D 456 " pdb=" C ILE D 456 " pdb=" CB ILE D 456 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 459 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 JDA D1001 " 0.016 2.00e-02 2.50e+03 1.82e-02 6.63e+00 pdb=" C11 JDA D1001 " 0.007 2.00e-02 2.50e+03 pdb=" C5 JDA D1001 " -0.022 2.00e-02 2.50e+03 pdb=" C6 JDA D1001 " -0.003 2.00e-02 2.50e+03 pdb=" C7 JDA D1001 " 0.007 2.00e-02 2.50e+03 pdb=" C8 JDA D1001 " 0.016 2.00e-02 2.50e+03 pdb=" C9 JDA D1001 " 0.015 2.00e-02 2.50e+03 pdb=" N3 JDA D1001 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 JDA D1001 " 0.011 2.00e-02 2.50e+03 1.53e-02 3.53e+00 pdb=" C13 JDA D1001 " -0.013 2.00e-02 2.50e+03 pdb=" C9 JDA D1001 " -0.021 2.00e-02 2.50e+03 pdb=" N3 JDA D1001 " 0.020 2.00e-02 2.50e+03 pdb=" N4 JDA D1001 " -0.011 2.00e-02 2.50e+03 pdb=" N5 JDA D1001 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N JDA D1001 " -0.006 2.00e-02 2.50e+03 9.88e-03 2.20e+00 pdb=" C JDA D1001 " 0.017 2.00e-02 2.50e+03 pdb=" C1 JDA D1001 " -0.005 2.00e-02 2.50e+03 pdb=" C14 JDA D1001 " 0.000 2.00e-02 2.50e+03 pdb=" C2 JDA D1001 " -0.012 2.00e-02 2.50e+03 pdb=" C3 JDA D1001 " 0.010 2.00e-02 2.50e+03 pdb=" C4 JDA D1001 " -0.002 2.00e-02 2.50e+03 pdb=" N1 JDA D1001 " 0.010 2.00e-02 2.50e+03 pdb=" N2 JDA D1001 " -0.013 2.00e-02 2.50e+03 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 502 2.76 - 3.30: 2577 3.30 - 3.83: 5125 3.83 - 4.37: 6393 4.37 - 4.90: 10494 Nonbonded interactions: 25091 Sorted by model distance: nonbonded pdb=" OE1 GLU D 202 " pdb=" O HOH D1101 " model vdw 2.231 3.040 nonbonded pdb=" O GLN D 431 " pdb=" NZ LYS D 523 " model vdw 2.234 3.120 nonbonded pdb=" O LEU C 73 " pdb=" OH TYR D 594 " model vdw 2.252 3.040 nonbonded pdb=" NH2 ARG D 450 " pdb=" OD2 ASP D 522 " model vdw 2.258 3.120 nonbonded pdb=" O GLU C 64 " pdb=" O HOH C 101 " model vdw 2.297 3.040 ... (remaining 25086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.660 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 0.030 2967 Z= 0.305 Angle : 0.627 6.849 4001 Z= 0.337 Chirality : 0.040 0.130 462 Planarity : 0.004 0.035 500 Dihedral : 13.897 79.170 1114 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: -0.97 (0.40), residues: 346 helix: -0.26 (0.43), residues: 119 sheet: -0.85 (0.41), residues: 103 loop : -0.54 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 747 HIS 0.003 0.001 HIS C 68 PHE 0.020 0.003 PHE D 505 TYR 0.011 0.002 TYR D 576 ARG 0.004 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.382 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 1.6289 time to fit residues: 79.9937 Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.110929 restraints weight = 3010.942| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.39 r_work: 0.3115 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2967 Z= 0.336 Angle : 0.621 6.764 4001 Z= 0.321 Chirality : 0.042 0.151 462 Planarity : 0.004 0.032 500 Dihedral : 6.288 49.252 393 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 6.33 % Favored : 91.27 % 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: 0.21 (0.42), residues: 346 helix: 1.02 (0.47), residues: 119 sheet: -0.37 (0.42), residues: 102 loop : -0.04 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 747 HIS 0.004 0.001 HIS C 68 PHE 0.020 0.003 PHE D 505 TYR 0.010 0.002 TYR D 512 ARG 0.003 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.344 Fit side-chains REVERT: D 483 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8003 (mttp) REVERT: D 526 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: D 761 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6528 (mptt) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 1.6989 time to fit residues: 86.7412 Evaluate side-chains 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 761 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112634 restraints weight = 2980.585| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.41 r_work: 0.3113 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2967 Z= 0.223 Angle : 0.528 5.523 4001 Z= 0.275 Chirality : 0.039 0.132 462 Planarity : 0.003 0.029 500 Dihedral : 5.994 45.983 393 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.71 % Allowed : 7.23 % Favored : 90.06 % 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: 0.76 (0.43), residues: 346 helix: 1.82 (0.49), residues: 113 sheet: -0.14 (0.43), residues: 102 loop : 0.03 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 747 HIS 0.002 0.001 HIS C 68 PHE 0.014 0.002 PHE D 505 TYR 0.008 0.002 TYR D 504 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.361 Fit side-chains REVERT: D 427 GLU cc_start: 0.8354 (mp0) cc_final: 0.8120 (mp0) REVERT: D 483 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.8032 (mttp) REVERT: D 754 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: D 759 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7592 (mm-30) REVERT: D 761 LYS cc_start: 0.7086 (mptt) cc_final: 0.6748 (ptmt) outliers start: 9 outliers final: 3 residues processed: 52 average time/residue: 1.6443 time to fit residues: 87.3613 Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 754 GLU Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111346 restraints weight = 3032.175| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.41 r_work: 0.3076 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2967 Z= 0.285 Angle : 0.558 5.310 4001 Z= 0.290 Chirality : 0.040 0.143 462 Planarity : 0.003 0.029 500 Dihedral : 6.014 44.953 393 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.31 % Allowed : 7.53 % Favored : 89.16 % 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: 0.90 (0.43), residues: 346 helix: 1.97 (0.49), residues: 113 sheet: -0.01 (0.44), residues: 102 loop : 0.01 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 487 HIS 0.003 0.001 HIS C 68 PHE 0.017 0.002 PHE D 505 TYR 0.010 0.002 TYR D 504 ARG 0.003 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.337 Fit side-chains REVERT: D 427 GLU cc_start: 0.8356 (mp0) cc_final: 0.8091 (mp0) REVERT: D 483 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7979 (mttp) REVERT: D 759 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7602 (mm-30) REVERT: D 761 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6718 (ptmt) outliers start: 11 outliers final: 4 residues processed: 54 average time/residue: 1.6798 time to fit residues: 92.6567 Evaluate side-chains 54 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 0.0370 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115317 restraints weight = 2984.104| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.39 r_work: 0.3175 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2967 Z= 0.141 Angle : 0.455 4.817 4001 Z= 0.240 Chirality : 0.037 0.124 462 Planarity : 0.003 0.026 500 Dihedral : 5.532 39.579 393 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.41 % Allowed : 8.43 % Favored : 89.16 % 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: 1.24 (0.44), residues: 346 helix: 2.50 (0.50), residues: 112 sheet: 0.04 (0.45), residues: 102 loop : 0.10 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 747 HIS 0.002 0.001 HIS D 111 PHE 0.008 0.001 PHE D 453 TYR 0.008 0.001 TYR D 504 ARG 0.001 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.339 Fit side-chains REVERT: D 427 GLU cc_start: 0.8346 (mp0) cc_final: 0.8126 (mp0) REVERT: D 483 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8028 (mttp) REVERT: D 761 LYS cc_start: 0.6824 (mptt) cc_final: 0.6577 (ptmt) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 1.5341 time to fit residues: 83.2523 Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112040 restraints weight = 3121.313| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.44 r_work: 0.3107 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2967 Z= 0.259 Angle : 0.530 4.863 4001 Z= 0.276 Chirality : 0.039 0.133 462 Planarity : 0.003 0.027 500 Dihedral : 5.745 40.795 393 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.01 % Allowed : 8.73 % Favored : 88.25 % 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: 1.23 (0.44), residues: 346 helix: 2.39 (0.49), residues: 113 sheet: 0.11 (0.45), residues: 102 loop : 0.12 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 747 HIS 0.003 0.001 HIS C 68 PHE 0.016 0.002 PHE D 505 TYR 0.009 0.002 TYR D 504 ARG 0.003 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: D 483 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.8007 (mttp) REVERT: D 761 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6596 (ptmt) outliers start: 10 outliers final: 4 residues processed: 55 average time/residue: 1.7014 time to fit residues: 95.5850 Evaluate side-chains 56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108806 restraints weight = 3026.165| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.52 r_work: 0.3077 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2967 Z= 0.235 Angle : 0.511 4.670 4001 Z= 0.267 Chirality : 0.038 0.130 462 Planarity : 0.003 0.028 500 Dihedral : 5.704 39.823 393 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.01 % Allowed : 8.73 % Favored : 88.25 % 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 (0.44), residues: 346 helix: 2.36 (0.49), residues: 112 sheet: 0.12 (0.45), residues: 102 loop : 0.14 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 747 HIS 0.003 0.001 HIS C 68 PHE 0.014 0.002 PHE D 505 TYR 0.009 0.002 TYR D 504 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: D 483 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7980 (mttp) REVERT: D 523 LYS cc_start: 0.8496 (tmtt) cc_final: 0.8272 (tmtt) REVERT: D 759 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7576 (mm-30) REVERT: D 761 LYS cc_start: 0.6864 (mptt) cc_final: 0.6548 (ptmt) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 1.5952 time to fit residues: 88.2613 Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.110006 restraints weight = 3056.040| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.54 r_work: 0.3122 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2967 Z= 0.179 Angle : 0.473 4.356 4001 Z= 0.247 Chirality : 0.037 0.125 462 Planarity : 0.003 0.027 500 Dihedral : 5.533 39.117 393 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.71 % Allowed : 9.64 % Favored : 87.65 % 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 (0.45), residues: 346 helix: 2.51 (0.49), residues: 112 sheet: 0.14 (0.46), residues: 102 loop : 0.21 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 747 HIS 0.002 0.001 HIS C 68 PHE 0.011 0.002 PHE D 505 TYR 0.008 0.001 TYR D 504 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: D 157 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7192 (mt-10) REVERT: D 483 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7966 (mttp) REVERT: D 759 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7559 (mm-30) REVERT: D 761 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6782 (ptmt) outliers start: 9 outliers final: 5 residues processed: 50 average time/residue: 1.6429 time to fit residues: 84.0163 Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109861 restraints weight = 3041.945| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.50 r_work: 0.3095 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2967 Z= 0.196 Angle : 0.484 4.344 4001 Z= 0.252 Chirality : 0.038 0.128 462 Planarity : 0.003 0.026 500 Dihedral : 5.546 39.086 393 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.01 % Allowed : 9.04 % Favored : 87.95 % 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 (0.45), residues: 346 helix: 2.49 (0.49), residues: 113 sheet: 0.13 (0.46), residues: 102 loop : 0.21 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 747 HIS 0.003 0.001 HIS C 68 PHE 0.013 0.002 PHE D 505 TYR 0.008 0.001 TYR D 504 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: D 483 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7967 (mttp) REVERT: D 759 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7562 (mm-30) REVERT: D 761 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6794 (ptmt) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 1.6427 time to fit residues: 87.3378 Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 ASN D 88 ASN D 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111106 restraints weight = 2999.467| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.49 r_work: 0.3142 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2967 Z= 0.167 Angle : 0.463 4.493 4001 Z= 0.242 Chirality : 0.037 0.125 462 Planarity : 0.003 0.025 500 Dihedral : 5.443 39.304 393 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 10.24 % Favored : 87.35 % 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: 1.44 (0.45), residues: 346 helix: 2.59 (0.49), residues: 113 sheet: 0.20 (0.48), residues: 96 loop : 0.22 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 747 HIS 0.002 0.001 HIS C 68 PHE 0.010 0.001 PHE D 505 TYR 0.008 0.001 TYR D 504 ARG 0.001 0.000 ARG C 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: D 157 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7155 (mt-10) REVERT: D 483 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7956 (mttp) REVERT: D 759 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7541 (mm-30) REVERT: D 761 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6835 (ptmt) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 1.7345 time to fit residues: 90.4007 Evaluate side-chains 54 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 761 LYS Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109405 restraints weight = 2978.166| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.47 r_work: 0.3084 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2967 Z= 0.265 Angle : 0.529 4.883 4001 Z= 0.274 Chirality : 0.039 0.138 462 Planarity : 0.003 0.027 500 Dihedral : 5.691 38.703 393 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.71 % Allowed : 10.24 % Favored : 87.05 % 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: 1.19 (0.44), residues: 346 helix: 2.03 (0.48), residues: 119 sheet: 0.16 (0.47), residues: 96 loop : 0.26 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 487 HIS 0.004 0.001 HIS C 68 PHE 0.016 0.002 PHE D 505 TYR 0.010 0.002 TYR D 504 ARG 0.003 0.000 ARG C 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2874.26 seconds wall clock time: 51 minutes 24.77 seconds (3084.77 seconds total)