Starting phenix.real_space_refine on Tue Mar 3 11:14:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh4_14721/03_2026/7zh4_14721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh4_14721/03_2026/7zh4_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zh4_14721/03_2026/7zh4_14721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh4_14721/03_2026/7zh4_14721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zh4_14721/03_2026/7zh4_14721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh4_14721/03_2026/7zh4_14721.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.72, per 1000 atoms: 0.24 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: 0.18 Conformation dependent library (CDL) restraints added in 73.0 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: 0.13 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: 0.47 Time building geometry restraints manager: 0.25 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: 1.800 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: 0.040 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.670 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- 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 : 4.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG C 42 TYR 0.011 0.002 TYR D 576 PHE 0.020 0.003 PHE D 505 TRP 0.005 0.002 TRP D 747 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 2967) covalent geometry : angle 0.62707 ( 4001) hydrogen bonds : bond 0.16020 ( 155) hydrogen bonds : angle 6.46111 ( 423) metal coordination : bond 0.03547 ( 4) metal coordination : angle 1.07784 ( 6) *********************** 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 : 0.114 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.7292 time to fit residues: 35.7195 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 : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.135037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111921 restraints weight = 3013.143| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.40 r_work: 0.3090 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0899 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= 0.174 Angle : 0.578 6.776 4007 Z= 0.299 Chirality : 0.040 0.141 462 Planarity : 0.004 0.031 500 Dihedral : 6.144 48.161 393 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.95 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.43), residues: 346 helix: 1.44 (0.48), residues: 113 sheet: -0.41 (0.42), residues: 102 loop : -0.10 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 42 TYR 0.008 0.002 TYR D 576 PHE 0.016 0.002 PHE D 505 TRP 0.005 0.002 TRP D 747 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 2967) covalent geometry : angle 0.57520 ( 4001) hydrogen bonds : bond 0.04460 ( 155) hydrogen bonds : angle 5.01775 ( 423) metal coordination : bond 0.00401 ( 4) metal coordination : angle 1.63570 ( 6) *********************** 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 : 0.124 Fit side-chains REVERT: D 483 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7958 (mttp) REVERT: D 761 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6758 (ptmt) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 0.7653 time to fit residues: 39.0475 Evaluate side-chains 48 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 0.3980 chunk 7 optimal weight: 0.0060 chunk 1 optimal weight: 3.9990 overall best weight: 0.8978 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.136573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113302 restraints weight = 3025.661| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.42 r_work: 0.3129 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2971 Z= 0.136 Angle : 0.512 5.733 4007 Z= 0.265 Chirality : 0.038 0.129 462 Planarity : 0.003 0.028 500 Dihedral : 5.852 44.167 393 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.11 % Allowed : 7.53 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.44), residues: 346 helix: 1.99 (0.49), residues: 113 sheet: -0.11 (0.43), residues: 102 loop : 0.03 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 42 TYR 0.007 0.001 TYR D 504 PHE 0.013 0.002 PHE D 505 TRP 0.004 0.001 TRP D 747 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2967) covalent geometry : angle 0.50871 ( 4001) hydrogen bonds : bond 0.03870 ( 155) hydrogen bonds : angle 4.63757 ( 423) metal coordination : bond 0.00331 ( 4) metal coordination : angle 1.63943 ( 6) *********************** 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 54 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.118 Fit side-chains REVERT: D 427 GLU cc_start: 0.8350 (mp0) cc_final: 0.8112 (mp0) REVERT: D 483 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.8017 (mttp) REVERT: D 523 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7919 (tmtt) REVERT: D 754 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: D 759 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 761 LYS cc_start: 0.7058 (mptt) cc_final: 0.6771 (ptmt) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.8108 time to fit residues: 41.3241 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 : 0.107 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.0050 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.135613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112353 restraints weight = 3037.735| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.41 r_work: 0.3133 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1257 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= 0.161 Angle : 0.528 4.994 4007 Z= 0.273 Chirality : 0.039 0.134 462 Planarity : 0.003 0.027 500 Dihedral : 5.812 42.345 393 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.01 % Allowed : 7.23 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.44), residues: 346 helix: 2.14 (0.49), residues: 113 sheet: 0.01 (0.44), residues: 102 loop : 0.02 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 42 TYR 0.009 0.002 TYR D 504 PHE 0.015 0.002 PHE D 505 TRP 0.005 0.002 TRP D 747 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2967) covalent geometry : angle 0.52550 ( 4001) hydrogen bonds : bond 0.03980 ( 155) hydrogen bonds : angle 4.57556 ( 423) metal coordination : bond 0.00362 ( 4) metal coordination : angle 1.53194 ( 6) *********************** 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 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.100 Fit side-chains REVERT: D 427 GLU cc_start: 0.8351 (mp0) cc_final: 0.8149 (mp0) REVERT: D 483 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8018 (mttp) REVERT: D 523 LYS cc_start: 0.8364 (tmtt) cc_final: 0.7988 (tttt) REVERT: D 759 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7599 (mm-30) REVERT: D 761 LYS cc_start: 0.6921 (mptt) cc_final: 0.6666 (ptmt) outliers start: 10 outliers final: 3 residues processed: 54 average time/residue: 0.7150 time to fit residues: 39.3144 Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 28 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.133078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109869 restraints weight = 3018.344| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.39 r_work: 0.3095 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 2971 Z= 0.292 Angle : 0.648 6.431 4007 Z= 0.333 Chirality : 0.044 0.150 462 Planarity : 0.004 0.030 500 Dihedral : 6.241 45.813 393 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.43), residues: 346 helix: 1.78 (0.49), residues: 113 sheet: -0.01 (0.44), residues: 102 loop : -0.05 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 42 TYR 0.015 0.003 TYR D 504 PHE 0.022 0.003 PHE D 505 TRP 0.008 0.003 TRP D 487 HIS 0.005 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 2967) covalent geometry : angle 0.64587 ( 4001) hydrogen bonds : bond 0.04949 ( 155) hydrogen bonds : angle 4.82646 ( 423) metal coordination : bond 0.00507 ( 4) metal coordination : angle 1.52345 ( 6) *********************** 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: 8 poor density : 52 time to evaluate : 0.119 Fit side-chains REVERT: D 483 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8035 (mttp) REVERT: D 759 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7577 (mm-30) outliers start: 8 outliers final: 3 residues processed: 55 average time/residue: 0.7458 time to fit residues: 41.8286 Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.122 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.134415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.109875 restraints weight = 2969.891| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.52 r_work: 0.3092 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2971 Z= 0.116 Angle : 0.482 4.688 4007 Z= 0.251 Chirality : 0.037 0.123 462 Planarity : 0.003 0.028 500 Dihedral : 5.729 42.262 393 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.41 % Allowed : 8.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.44), residues: 346 helix: 2.30 (0.49), residues: 112 sheet: 0.04 (0.44), residues: 102 loop : 0.14 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 42 TYR 0.009 0.001 TYR D 504 PHE 0.010 0.001 PHE D 505 TRP 0.003 0.001 TRP D 567 HIS 0.002 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2967) covalent geometry : angle 0.47833 ( 4001) hydrogen bonds : bond 0.03585 ( 155) hydrogen bonds : angle 4.36205 ( 423) metal coordination : bond 0.00317 ( 4) metal coordination : angle 1.70009 ( 6) *********************** 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 54 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.086 Fit side-chains REVERT: D 483 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8008 (mttp) REVERT: D 759 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7557 (mm-30) REVERT: D 761 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6655 (ptmt) outliers start: 8 outliers final: 2 residues processed: 49 average time/residue: 0.7208 time to fit residues: 36.0040 Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.135975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112924 restraints weight = 3067.415| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.40 r_work: 0.3115 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1414 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= 0.148 Angle : 0.504 4.762 4007 Z= 0.260 Chirality : 0.038 0.128 462 Planarity : 0.003 0.027 500 Dihedral : 5.715 40.747 393 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.44), residues: 346 helix: 2.33 (0.49), residues: 112 sheet: 0.10 (0.45), residues: 102 loop : 0.21 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 42 TYR 0.009 0.002 TYR D 504 PHE 0.014 0.002 PHE D 505 TRP 0.004 0.001 TRP D 487 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2967) covalent geometry : angle 0.50028 ( 4001) hydrogen bonds : bond 0.03789 ( 155) hydrogen bonds : angle 4.35519 ( 423) metal coordination : bond 0.00349 ( 4) metal coordination : angle 1.55221 ( 6) *********************** 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 55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: D 483 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7993 (mttp) REVERT: D 759 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7572 (mm-30) REVERT: D 761 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6419 (mptt) outliers start: 9 outliers final: 3 residues processed: 51 average time/residue: 0.6787 time to fit residues: 35.2890 Evaluate side-chains 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.077 ------------------------------------------------------------------------------- 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 483 LYS 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 0 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.132625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108233 restraints weight = 3070.783| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.50 r_work: 0.3050 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2971 Z= 0.198 Angle : 0.554 5.467 4007 Z= 0.285 Chirality : 0.040 0.137 462 Planarity : 0.003 0.029 500 Dihedral : 5.901 41.542 393 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.44 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.44), residues: 346 helix: 2.12 (0.48), residues: 113 sheet: 0.07 (0.45), residues: 102 loop : 0.14 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 42 TYR 0.011 0.002 TYR D 504 PHE 0.018 0.002 PHE D 505 TRP 0.006 0.002 TRP D 487 HIS 0.004 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 2967) covalent geometry : angle 0.55163 ( 4001) hydrogen bonds : bond 0.04208 ( 155) hydrogen bonds : angle 4.48881 ( 423) metal coordination : bond 0.00401 ( 4) metal coordination : angle 1.44551 ( 6) *********************** 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 58 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: D 483 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8039 (mttp) REVERT: D 565 GLU cc_start: 0.8292 (tp30) cc_final: 0.8033 (tp30) REVERT: D 759 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7568 (mm-30) REVERT: D 761 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6383 (mptt) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.7326 time to fit residues: 39.5497 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.134582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.110154 restraints weight = 3036.282| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.50 r_work: 0.3114 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2971 Z= 0.121 Angle : 0.481 4.230 4007 Z= 0.249 Chirality : 0.037 0.125 462 Planarity : 0.003 0.028 500 Dihedral : 5.619 39.010 393 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.81 % Allowed : 10.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.45), residues: 346 helix: 2.43 (0.49), residues: 113 sheet: 0.08 (0.45), residues: 102 loop : 0.21 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 42 TYR 0.008 0.001 TYR D 504 PHE 0.011 0.002 PHE D 505 TRP 0.003 0.001 TRP D 747 HIS 0.002 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2967) covalent geometry : angle 0.47680 ( 4001) hydrogen bonds : bond 0.03537 ( 155) hydrogen bonds : angle 4.23445 ( 423) metal coordination : bond 0.00336 ( 4) metal coordination : angle 1.65303 ( 6) *********************** 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 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.095 Fit side-chains REVERT: D 118 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.5722 (pmt-80) REVERT: D 483 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7973 (mttp) REVERT: D 759 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7567 (mm-30) REVERT: D 761 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6482 (mptt) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.7452 time to fit residues: 37.2783 Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 483 LYS 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 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5736 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.136189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111726 restraints weight = 3057.563| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.50 r_work: 0.3141 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1625 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= 0.101 Angle : 0.455 4.436 4007 Z= 0.236 Chirality : 0.037 0.121 462 Planarity : 0.003 0.026 500 Dihedral : 5.403 39.369 393 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.81 % Allowed : 10.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.45), residues: 346 helix: 2.62 (0.50), residues: 113 sheet: 0.15 (0.46), residues: 102 loop : 0.24 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 42 TYR 0.008 0.001 TYR D 504 PHE 0.009 0.001 PHE D 505 TRP 0.004 0.001 TRP D 747 HIS 0.002 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 2967) covalent geometry : angle 0.45006 ( 4001) hydrogen bonds : bond 0.03241 ( 155) hydrogen bonds : angle 4.04608 ( 423) metal coordination : bond 0.00334 ( 4) metal coordination : angle 1.77693 ( 6) ********************** 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: 6 poor density : 47 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: D 759 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7459 (mm-30) REVERT: D 761 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6814 (ptmt) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.7934 time to fit residues: 41.2620 Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 7 optimal weight: 0.0980 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.136365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.112041 restraints weight = 3012.156| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.47 r_work: 0.3151 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1729 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= 0.104 Angle : 0.470 4.243 4007 Z= 0.242 Chirality : 0.037 0.122 462 Planarity : 0.003 0.025 500 Dihedral : 5.309 39.346 393 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.81 % Allowed : 10.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.45), residues: 346 helix: 2.62 (0.49), residues: 113 sheet: 0.17 (0.46), residues: 102 loop : 0.35 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 42 TYR 0.008 0.001 TYR D 504 PHE 0.010 0.001 PHE D 505 TRP 0.003 0.001 TRP D 747 HIS 0.002 0.001 HIS D 511 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 2967) covalent geometry : angle 0.46522 ( 4001) hydrogen bonds : bond 0.03241 ( 155) hydrogen bonds : angle 4.00647 ( 423) metal coordination : bond 0.00349 ( 4) metal coordination : angle 1.76543 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.02 seconds wall clock time: 24 minutes 24.51 seconds (1464.51 seconds total)