Starting phenix.real_space_refine on Wed Jul 23 10:09:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh4_14721/07_2025/7zh4_14721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh4_14721/07_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_14721/07_2025/7zh4_14721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh4_14721/07_2025/7zh4_14721.map" model { file = "/net/cci-nas-00/data/ceres_data/7zh4_14721/07_2025/7zh4_14721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh4_14721/07_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-5711/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: 3.17, per 1000 atoms: 1.07 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: 0.73 Conformation dependent library (CDL) restraints added in 321.0 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: 0.47 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: 0.95 Time building geometry restraints manager: 0.81 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.210 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:15.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- 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 0.059 2971 Z= 0.207 Angle : 0.628 6.849 4007 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 Details of bonding type rmsd hydrogen bonds : bond 0.16020 ( 155) hydrogen bonds : angle 6.46111 ( 423) metal coordination : bond 0.03547 ( 4) metal coordination : angle 1.07784 ( 6) covalent geometry : bond 0.00457 ( 2967) covalent geometry : angle 0.62707 ( 4001) *********************** 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 : 0.371 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 1.5696 time to fit residues: 77.1037 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 : 0.354 ------------------------------------------------------------------------------- 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: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.134019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.110870 restraints weight = 3010.365| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.40 r_work: 0.3092 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 2971 Z= 0.222 Angle : 0.622 6.827 4007 Z= 0.320 Chirality : 0.042 0.150 462 Planarity : 0.004 0.032 500 Dihedral : 6.288 49.247 393 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 6.02 % Favored : 91.57 % 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: 1.01 (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 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 155) hydrogen bonds : angle 5.11401 ( 423) metal coordination : bond 0.00517 ( 4) metal coordination : angle 1.51268 ( 6) covalent geometry : bond 0.00509 ( 2967) covalent geometry : angle 0.62011 ( 4001) *********************** 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 : 0.379 Fit side-chains REVERT: D 483 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8006 (mttp) REVERT: D 526 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: D 761 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6527 (mptt) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 1.6646 time to fit residues: 85.0525 Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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: 0.3980 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.135577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.112435 restraints weight = 2978.243| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.40 r_work: 0.3141 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2971 Z= 0.160 Angle : 0.539 5.397 4007 Z= 0.279 Chirality : 0.039 0.134 462 Planarity : 0.003 0.029 500 Dihedral : 6.017 46.153 393 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.01 % Allowed : 6.93 % 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: 0.73 (0.43), residues: 346 helix: 1.78 (0.49), residues: 113 sheet: -0.15 (0.43), residues: 102 loop : 0.02 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 747 HIS 0.003 0.001 HIS C 68 PHE 0.015 0.002 PHE D 505 TYR 0.008 0.002 TYR D 576 ARG 0.003 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 155) hydrogen bonds : angle 4.74134 ( 423) metal coordination : bond 0.00348 ( 4) metal coordination : angle 1.53113 ( 6) covalent geometry : bond 0.00359 ( 2967) covalent geometry : angle 0.53622 ( 4001) *********************** 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 58 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.382 Fit side-chains REVERT: D 427 GLU cc_start: 0.8353 (mp0) cc_final: 0.8124 (mp0) REVERT: D 483 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8034 (mttp) REVERT: D 754 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7891 (pt0) REVERT: D 759 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7596 (mm-30) REVERT: D 761 LYS cc_start: 0.7117 (mptt) cc_final: 0.6779 (ptmt) outliers start: 10 outliers final: 3 residues processed: 53 average time/residue: 1.6721 time to fit residues: 90.5921 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 : 0.367 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.137212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113974 restraints weight = 3018.166| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.41 r_work: 0.3113 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2971 Z= 0.115 Angle : 0.484 4.923 4007 Z= 0.252 Chirality : 0.037 0.125 462 Planarity : 0.003 0.027 500 Dihedral : 5.679 41.789 393 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.71 % Allowed : 7.83 % Favored : 89.46 % 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: 1.13 (0.44), residues: 346 helix: 2.29 (0.50), residues: 112 sheet: 0.05 (0.44), residues: 102 loop : 0.09 (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 C 68 PHE 0.010 0.001 PHE D 505 TYR 0.007 0.001 TYR D 504 ARG 0.002 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 155) hydrogen bonds : angle 4.43449 ( 423) metal coordination : bond 0.00384 ( 4) metal coordination : angle 1.71911 ( 6) covalent geometry : bond 0.00253 ( 2967) covalent geometry : angle 0.47982 ( 4001) *********************** 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 59 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.298 Fit side-chains REVERT: D 427 GLU cc_start: 0.8366 (mp0) cc_final: 0.8138 (mp0) REVERT: D 483 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.8002 (mttp) REVERT: D 759 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7600 (mm-30) REVERT: D 761 LYS cc_start: 0.6868 (mptt) cc_final: 0.6621 (ptmt) outliers start: 9 outliers final: 3 residues processed: 53 average time/residue: 1.6201 time to fit residues: 87.7256 Evaluate side-chains 55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.135210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.112003 restraints weight = 3017.246| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.40 r_work: 0.3106 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2971 Z= 0.172 Angle : 0.531 4.885 4007 Z= 0.274 Chirality : 0.039 0.130 462 Planarity : 0.003 0.028 500 Dihedral : 5.823 42.045 393 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.71 % Allowed : 8.43 % Favored : 88.86 % 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 (0.44), residues: 346 helix: 2.24 (0.49), residues: 113 sheet: 0.10 (0.45), residues: 102 loop : 0.10 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 487 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 0.002 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 155) hydrogen bonds : angle 4.50425 ( 423) metal coordination : bond 0.00358 ( 4) metal coordination : angle 1.51075 ( 6) covalent geometry : bond 0.00390 ( 2967) covalent geometry : angle 0.52793 ( 4001) *********************** 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 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.369 Fit side-chains REVERT: D 427 GLU cc_start: 0.8356 (mp0) cc_final: 0.8116 (mp0) REVERT: D 483 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8026 (mttp) REVERT: D 759 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7588 (mm-30) REVERT: D 761 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6644 (ptmt) outliers start: 9 outliers final: 4 residues processed: 54 average time/residue: 1.6724 time to fit residues: 92.2648 Evaluate side-chains 55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.134384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110965 restraints weight = 3136.700| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.43 r_work: 0.3109 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2971 Z= 0.210 Angle : 0.562 5.325 4007 Z= 0.290 Chirality : 0.040 0.137 462 Planarity : 0.003 0.029 500 Dihedral : 5.957 42.871 393 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.71 % Allowed : 8.73 % Favored : 88.55 % 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: 1.05 (0.44), residues: 346 helix: 2.08 (0.49), residues: 113 sheet: 0.09 (0.45), residues: 102 loop : 0.10 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 487 HIS 0.004 0.001 HIS C 68 PHE 0.018 0.002 PHE D 505 TYR 0.011 0.002 TYR D 504 ARG 0.003 0.001 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 155) hydrogen bonds : angle 4.55988 ( 423) metal coordination : bond 0.00389 ( 4) metal coordination : angle 1.46175 ( 6) covalent geometry : bond 0.00483 ( 2967) covalent geometry : angle 0.55952 ( 4001) *********************** 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: 9 poor density : 51 time to evaluate : 0.331 Fit side-chains REVERT: D 483 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7973 (mttp) REVERT: D 759 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7600 (mm-30) REVERT: D 761 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6666 (ptmt) outliers start: 9 outliers final: 4 residues processed: 54 average time/residue: 1.6539 time to fit residues: 91.2383 Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.134387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.110024 restraints weight = 3015.836| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.49 r_work: 0.3116 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2971 Z= 0.126 Angle : 0.482 4.161 4007 Z= 0.250 Chirality : 0.037 0.123 462 Planarity : 0.003 0.027 500 Dihedral : 5.645 40.138 393 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.61 % Allowed : 8.43 % 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: 1.27 (0.44), residues: 346 helix: 2.41 (0.49), residues: 113 sheet: 0.11 (0.45), residues: 102 loop : 0.18 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 487 HIS 0.002 0.001 HIS C 68 PHE 0.011 0.002 PHE D 505 TYR 0.009 0.001 TYR D 504 ARG 0.002 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 155) hydrogen bonds : angle 4.28754 ( 423) metal coordination : bond 0.00264 ( 4) metal coordination : angle 1.72558 ( 6) covalent geometry : bond 0.00279 ( 2967) covalent geometry : angle 0.47736 ( 4001) *********************** 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 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: D 483 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7974 (mttp) REVERT: D 565 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8027 (tp30) REVERT: D 759 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7554 (mm-30) REVERT: D 761 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6747 (ptmt) outliers start: 12 outliers final: 5 residues processed: 53 average time/residue: 1.6217 time to fit residues: 87.8793 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 : 0.360 ------------------------------------------------------------------------------- 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 486 ARG Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 761 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: 2.9990 chunk 3 optimal weight: 0.0030 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.133827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109489 restraints weight = 3059.265| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.49 r_work: 0.3105 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2971 Z= 0.153 Angle : 0.508 4.687 4007 Z= 0.262 Chirality : 0.038 0.128 462 Planarity : 0.003 0.027 500 Dihedral : 5.695 39.367 393 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.31 % Allowed : 9.04 % 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: 1.28 (0.44), residues: 346 helix: 2.36 (0.49), residues: 113 sheet: 0.15 (0.46), residues: 102 loop : 0.21 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 487 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 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 155) hydrogen bonds : angle 4.33987 ( 423) metal coordination : bond 0.00348 ( 4) metal coordination : angle 1.60074 ( 6) covalent geometry : bond 0.00345 ( 2967) covalent geometry : angle 0.50460 ( 4001) *********************** 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 59 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: D 483 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7974 (mttp) REVERT: D 759 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7564 (mm-30) REVERT: D 761 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6756 (ptmt) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 1.5731 time to fit residues: 83.7118 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 : 0.334 ------------------------------------------------------------------------------- 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 486 ARG 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: 0.9980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.0270 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.135706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111404 restraints weight = 3035.085| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.48 r_work: 0.3112 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2971 Z= 0.106 Angle : 0.460 4.312 4007 Z= 0.239 Chirality : 0.037 0.122 462 Planarity : 0.003 0.026 500 Dihedral : 5.456 39.241 393 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 1.42 (0.45), residues: 346 helix: 2.57 (0.49), residues: 113 sheet: 0.17 (0.46), residues: 102 loop : 0.24 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 747 HIS 0.002 0.001 HIS D 511 PHE 0.009 0.001 PHE D 505 TYR 0.008 0.001 TYR D 504 ARG 0.001 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 155) hydrogen bonds : angle 4.12749 ( 423) metal coordination : bond 0.00378 ( 4) metal coordination : angle 1.78880 ( 6) covalent geometry : bond 0.00231 ( 2967) covalent geometry : angle 0.45483 ( 4001) *********************** 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 56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.361 Fit side-chains REVERT: D 118 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.5469 (pmt-80) REVERT: D 483 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7967 (mttp) REVERT: D 759 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7516 (mm-30) REVERT: D 761 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6787 (ptmt) outliers start: 9 outliers final: 4 residues processed: 51 average time/residue: 1.7397 time to fit residues: 90.5519 Evaluate side-chains 56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 486 ARG 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: 5.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.134732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110352 restraints weight = 2994.413| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.48 r_work: 0.3094 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2971 Z= 0.134 Angle : 0.492 4.228 4007 Z= 0.254 Chirality : 0.038 0.125 462 Planarity : 0.003 0.026 500 Dihedral : 5.521 38.958 393 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.41 % Allowed : 9.64 % 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: 1.40 (0.45), residues: 346 helix: 2.52 (0.49), residues: 113 sheet: 0.17 (0.46), residues: 102 loop : 0.25 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 487 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 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 155) hydrogen bonds : angle 4.18385 ( 423) metal coordination : bond 0.00331 ( 4) metal coordination : angle 1.61532 ( 6) covalent geometry : bond 0.00300 ( 2967) covalent geometry : angle 0.48810 ( 4001) ********************** 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 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.333 Fit side-chains REVERT: D 118 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.5539 (pmt-80) REVERT: D 483 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7964 (mttp) REVERT: D 759 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7556 (mm-30) REVERT: D 761 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6745 (ptmt) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 1.7131 time to fit residues: 85.7092 Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 486 ARG 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: 0.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 32 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.134607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.110169 restraints weight = 2973.054| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.49 r_work: 0.3117 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2971 Z= 0.150 Angle : 0.503 4.633 4007 Z= 0.260 Chirality : 0.038 0.128 462 Planarity : 0.003 0.027 500 Dihedral : 5.609 38.858 393 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 1.25 (0.44), residues: 346 helix: 2.12 (0.48), residues: 119 sheet: 0.17 (0.45), residues: 102 loop : 0.30 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 155) hydrogen bonds : angle 4.23222 ( 423) metal coordination : bond 0.00346 ( 4) metal coordination : angle 1.55801 ( 6) covalent geometry : bond 0.00339 ( 2967) covalent geometry : angle 0.49949 ( 4001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3046.61 seconds wall clock time: 52 minutes 47.49 seconds (3167.49 seconds total)