Starting phenix.real_space_refine on Mon Sep 23 13:23:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/09_2024/6x0u_21984.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/09_2024/6x0u_21984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/09_2024/6x0u_21984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/09_2024/6x0u_21984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/09_2024/6x0u_21984.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/09_2024/6x0u_21984.cif" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 1942 2.51 5 N 544 2.21 5 O 587 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3091 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 933 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1220 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain breaks: 4 Chain: "A" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 484 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Time building chain proxies: 3.21, per 1000 atoms: 1.04 Number of scatterers: 3091 At special positions: 0 Unit cell: (99.456, 83.916, 81.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 587 8.00 N 544 7.00 C 1942 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: 0.80 Conformation dependent library (CDL) restraints added in 376.8 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 68.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 8 through 21 removed outlier: 3.826A pdb=" N GLN B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 21 " --> pdb=" O CYS B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 removed outlier: 3.612A pdb=" N ARG B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 65 removed outlier: 3.870A pdb=" N VAL B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 85 removed outlier: 4.061A pdb=" N SER B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS B 82 " --> pdb=" O HIS B 78 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 removed outlier: 4.107A pdb=" N ILE B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 removed outlier: 3.684A pdb=" N PHE D 8 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 51 removed outlier: 3.902A pdb=" N LYS D 39 " --> pdb=" O ARG D 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.578A pdb=" N LEU D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 3.642A pdb=" N ALA D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 115 removed outlier: 3.537A pdb=" N ASP D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 183 removed outlier: 4.098A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 175 " --> pdb=" O CYS D 171 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D 176 " --> pdb=" O HIS D 172 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.769A pdb=" N THR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 54 removed outlier: 3.654A pdb=" N SER A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 75 removed outlier: 3.833A pdb=" N SER A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 34 removed outlier: 3.531A pdb=" N MET C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 28 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 29 " --> pdb=" O MET C 25 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 removed outlier: 3.808A pdb=" N GLY C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 75 removed outlier: 3.862A pdb=" N LEU C 60 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 408 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: 0.61 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1050 1.34 - 1.46: 519 1.46 - 1.58: 1526 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3121 Sorted by residual: bond pdb=" N ASN D 135 " pdb=" CA ASN D 135 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.60e+00 bond pdb=" N ASN D 136 " pdb=" CA ASN D 136 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.28e-01 bond pdb=" CA VAL B 28 " pdb=" CB VAL B 28 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.11e-02 8.12e+03 6.79e-01 bond pdb=" CA VAL B 86 " pdb=" C VAL B 86 " ideal model delta sigma weight residual 1.525 1.515 0.010 1.29e-02 6.01e+03 6.25e-01 bond pdb=" CG LEU B 96 " pdb=" CD1 LEU B 96 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.13e-01 ... (remaining 3116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 4119 1.77 - 3.53: 76 3.53 - 5.30: 8 5.30 - 7.06: 1 7.06 - 8.83: 1 Bond angle restraints: 4205 Sorted by residual: angle pdb=" C ASN D 135 " pdb=" CA ASN D 135 " pdb=" CB ASN D 135 " ideal model delta sigma weight residual 110.42 115.77 -5.35 1.99e+00 2.53e-01 7.22e+00 angle pdb=" CA LEU D 82 " pdb=" CB LEU D 82 " pdb=" CG LEU D 82 " ideal model delta sigma weight residual 116.30 125.13 -8.83 3.50e+00 8.16e-02 6.36e+00 angle pdb=" N ARG D 141 " pdb=" CA ARG D 141 " pdb=" C ARG D 141 " ideal model delta sigma weight residual 111.96 108.82 3.14 1.41e+00 5.03e-01 4.94e+00 angle pdb=" N ASN D 135 " pdb=" CA ASN D 135 " pdb=" CB ASN D 135 " ideal model delta sigma weight residual 110.49 106.91 3.58 1.69e+00 3.50e-01 4.49e+00 angle pdb=" N ASP A 26 " pdb=" CA ASP A 26 " pdb=" C ASP A 26 " ideal model delta sigma weight residual 113.41 111.00 2.41 1.22e+00 6.72e-01 3.89e+00 ... (remaining 4200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 1738 17.60 - 35.20: 171 35.20 - 52.80: 34 52.80 - 70.39: 5 70.39 - 87.99: 2 Dihedral angle restraints: 1950 sinusoidal: 794 harmonic: 1156 Sorted by residual: dihedral pdb=" CA LEU D 134 " pdb=" C LEU D 134 " pdb=" N ASN D 135 " pdb=" CA ASN D 135 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE D 133 " pdb=" C PHE D 133 " pdb=" N LEU D 134 " pdb=" CA LEU D 134 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ASN D 135 " pdb=" C ASN D 135 " pdb=" N ASN D 136 " pdb=" CA ASN D 136 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 1947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 247 0.024 - 0.048: 175 0.048 - 0.072: 56 0.072 - 0.096: 18 0.096 - 0.120: 9 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA PRO B 123 " pdb=" N PRO B 123 " pdb=" C PRO B 123 " pdb=" CB PRO B 123 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA PRO B 9 " pdb=" N PRO B 9 " pdb=" C PRO B 9 " pdb=" CB PRO B 9 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.09e-01 chirality pdb=" CA VAL D 143 " pdb=" N VAL D 143 " pdb=" C VAL D 143 " pdb=" CB VAL D 143 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 502 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 122 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO B 123 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 185 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO D 186 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 186 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 186 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 8 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.35e-01 pdb=" N PRO B 9 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 9 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 9 " 0.014 5.00e-02 4.00e+02 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 872 2.80 - 3.33: 2848 3.33 - 3.85: 4253 3.85 - 4.38: 5348 4.38 - 4.90: 8717 Nonbonded interactions: 22038 Sorted by model distance: nonbonded pdb=" O PRO A 57 " pdb=" OG SER A 61 " model vdw 2.277 3.040 nonbonded pdb=" O ALA C 59 " pdb=" OG SER C 62 " model vdw 2.283 3.040 nonbonded pdb=" OE1 GLN B 84 " pdb=" OG1 THR A 24 " model vdw 2.301 3.040 nonbonded pdb=" O ALA B 115 " pdb=" NE2 GLN B 120 " model vdw 2.310 3.120 nonbonded pdb=" O GLY B 40 " pdb=" OG SER B 41 " model vdw 2.332 3.040 ... (remaining 22033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 75) selection = chain 'C' } 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 group one per residue 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: 2.030 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.490 Find NCS groups from input model: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.004 0.024 3121 Z= 0.257 Angle : 0.618 8.827 4205 Z= 0.348 Chirality : 0.037 0.120 505 Planarity : 0.003 0.033 540 Dihedral : 14.498 87.993 1190 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.68 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: -5.79 (0.33), residues: 380 helix: -4.35 (0.17), residues: 263 sheet: None (None), residues: 0 loop : -1.86 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 91 HIS 0.002 0.001 HIS D 172 PHE 0.010 0.002 PHE D 156 TYR 0.012 0.002 TYR B 114 ARG 0.003 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.371 Fit side-chains REVERT: B 88 LYS cc_start: 0.8241 (tppt) cc_final: 0.7685 (tttp) REVERT: D 35 ARG cc_start: 0.5999 (tpt170) cc_final: 0.5711 (tpt170) REVERT: D 69 LYS cc_start: 0.8324 (mttt) cc_final: 0.7534 (tptm) REVERT: D 151 ASP cc_start: 0.8158 (t0) cc_final: 0.7876 (t0) REVERT: D 167 GLU cc_start: 0.8421 (mp0) cc_final: 0.7168 (pt0) REVERT: A 41 MET cc_start: 0.8843 (tpt) cc_final: 0.8513 (tpp) REVERT: C 36 ASN cc_start: 0.7971 (t0) cc_final: 0.7761 (m-40) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2600 time to fit residues: 33.1975 Evaluate side-chains 79 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 82 HIS D 48 ASN D 176 GLN C 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3121 Z= 0.271 Angle : 0.664 8.011 4205 Z= 0.332 Chirality : 0.040 0.143 505 Planarity : 0.005 0.041 540 Dihedral : 4.784 18.027 423 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.46 % Allowed : 17.84 % Favored : 80.70 % 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: -4.18 (0.35), residues: 380 helix: -2.65 (0.24), residues: 275 sheet: None (None), residues: 0 loop : -2.46 (0.56), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 91 HIS 0.003 0.001 HIS B 82 PHE 0.007 0.002 PHE D 156 TYR 0.011 0.002 TYR B 95 ARG 0.004 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.344 Fit side-chains REVERT: B 66 ARG cc_start: 0.7206 (mtm180) cc_final: 0.6904 (mtm-85) REVERT: B 88 LYS cc_start: 0.8172 (tppt) cc_final: 0.7649 (tttp) REVERT: B 114 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.6128 (p90) REVERT: D 42 TYR cc_start: 0.7716 (m-80) cc_final: 0.6795 (m-80) REVERT: D 95 GLU cc_start: 0.8026 (tt0) cc_final: 0.7793 (tt0) REVERT: D 167 GLU cc_start: 0.8568 (mp0) cc_final: 0.7269 (pt0) REVERT: A 41 MET cc_start: 0.8775 (tpt) cc_final: 0.8453 (tpp) REVERT: C 58 GLU cc_start: 0.7629 (mp0) cc_final: 0.7208 (mp0) REVERT: C 67 LEU cc_start: 0.8136 (mm) cc_final: 0.7699 (mt) REVERT: C 69 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8246 (tppt) outliers start: 5 outliers final: 3 residues processed: 95 average time/residue: 0.2155 time to fit residues: 23.4412 Evaluate side-chains 83 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain C residue 32 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.0070 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3121 Z= 0.122 Angle : 0.518 7.105 4205 Z= 0.258 Chirality : 0.034 0.121 505 Planarity : 0.003 0.034 540 Dihedral : 4.009 18.690 423 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.51 % Allowed : 20.47 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.41), residues: 380 helix: -0.91 (0.30), residues: 272 sheet: None (None), residues: 0 loop : -2.13 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 91 HIS 0.001 0.000 HIS B 78 PHE 0.006 0.001 PHE D 133 TYR 0.006 0.001 TYR B 95 ARG 0.004 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.349 Fit side-chains REVERT: B 24 SER cc_start: 0.8486 (m) cc_final: 0.8052 (p) REVERT: B 66 ARG cc_start: 0.7192 (mtm180) cc_final: 0.6887 (mtm-85) REVERT: B 88 LYS cc_start: 0.8183 (tppt) cc_final: 0.7641 (tttp) REVERT: B 114 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.5499 (p90) REVERT: D 134 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7356 (mt) REVERT: A 41 MET cc_start: 0.8621 (tpt) cc_final: 0.8400 (tpp) REVERT: A 49 ARG cc_start: 0.7442 (mtt180) cc_final: 0.6041 (mmt180) REVERT: C 36 ASN cc_start: 0.8085 (t0) cc_final: 0.7683 (t0) REVERT: C 69 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8212 (tppt) outliers start: 12 outliers final: 3 residues processed: 96 average time/residue: 0.2342 time to fit residues: 25.3380 Evaluate side-chains 90 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.0000 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3121 Z= 0.169 Angle : 0.553 9.672 4205 Z= 0.271 Chirality : 0.036 0.120 505 Planarity : 0.003 0.031 540 Dihedral : 3.998 17.049 423 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.51 % Allowed : 21.35 % Favored : 75.15 % 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: -1.46 (0.43), residues: 380 helix: -0.42 (0.32), residues: 282 sheet: None (None), residues: 0 loop : -2.29 (0.56), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 91 HIS 0.001 0.000 HIS B 78 PHE 0.006 0.001 PHE B 52 TYR 0.010 0.001 TYR B 95 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.370 Fit side-chains REVERT: B 24 SER cc_start: 0.8451 (m) cc_final: 0.8224 (p) REVERT: B 66 ARG cc_start: 0.7255 (mtm180) cc_final: 0.6919 (mtm-85) REVERT: B 114 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.5585 (p90) REVERT: D 42 TYR cc_start: 0.7531 (m-80) cc_final: 0.6786 (m-80) REVERT: D 167 GLU cc_start: 0.8808 (mm-30) cc_final: 0.7176 (pt0) REVERT: D 172 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7758 (t-90) REVERT: A 41 MET cc_start: 0.8705 (tpt) cc_final: 0.8406 (tpp) REVERT: A 49 ARG cc_start: 0.7639 (mtt180) cc_final: 0.5995 (mmt180) REVERT: C 36 ASN cc_start: 0.8092 (t0) cc_final: 0.7699 (m-40) REVERT: C 69 LYS cc_start: 0.8423 (mtpt) cc_final: 0.8205 (tppt) outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 0.2190 time to fit residues: 22.7392 Evaluate side-chains 90 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3121 Z= 0.209 Angle : 0.564 7.264 4205 Z= 0.278 Chirality : 0.038 0.116 505 Planarity : 0.003 0.033 540 Dihedral : 4.145 17.692 423 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.22 % Allowed : 23.68 % Favored : 73.10 % 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: -1.10 (0.43), residues: 380 helix: -0.13 (0.32), residues: 282 sheet: None (None), residues: 0 loop : -2.27 (0.56), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 91 HIS 0.001 0.000 HIS B 127 PHE 0.008 0.001 PHE B 52 TYR 0.011 0.002 TYR B 95 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.330 Fit side-chains REVERT: B 24 SER cc_start: 0.8600 (m) cc_final: 0.8249 (p) REVERT: B 66 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6947 (mtm-85) REVERT: B 88 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8137 (tttp) REVERT: B 114 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.5879 (p90) REVERT: D 135 ASN cc_start: 0.6685 (m-40) cc_final: 0.6376 (p0) REVERT: D 172 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.7946 (t-90) REVERT: A 41 MET cc_start: 0.8817 (tpt) cc_final: 0.8281 (tpp) REVERT: A 49 ARG cc_start: 0.7764 (mtt180) cc_final: 0.6278 (mmt180) REVERT: C 30 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6428 (tp30) REVERT: C 36 ASN cc_start: 0.8102 (t0) cc_final: 0.7734 (m-40) REVERT: C 69 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8278 (tppt) outliers start: 11 outliers final: 6 residues processed: 85 average time/residue: 0.2368 time to fit residues: 22.6991 Evaluate side-chains 84 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3121 Z= 0.143 Angle : 0.521 7.089 4205 Z= 0.254 Chirality : 0.036 0.117 505 Planarity : 0.003 0.033 540 Dihedral : 3.836 17.466 423 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.22 % Allowed : 23.10 % Favored : 73.68 % 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: -0.34 (0.44), residues: 380 helix: 0.47 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -2.04 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 91 HIS 0.001 0.000 HIS B 78 PHE 0.006 0.001 PHE D 133 TYR 0.008 0.001 TYR B 95 ARG 0.003 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.360 Fit side-chains REVERT: B 24 SER cc_start: 0.8580 (m) cc_final: 0.8281 (p) REVERT: B 66 ARG cc_start: 0.7276 (mtm180) cc_final: 0.6920 (mtm-85) REVERT: B 114 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.5737 (p90) REVERT: D 135 ASN cc_start: 0.6547 (OUTLIER) cc_final: 0.6203 (p0) REVERT: D 172 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7937 (t-90) REVERT: A 41 MET cc_start: 0.8747 (tpt) cc_final: 0.8230 (tpp) REVERT: A 49 ARG cc_start: 0.7727 (mtt180) cc_final: 0.6191 (mmt180) REVERT: C 30 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6379 (tp30) REVERT: C 36 ASN cc_start: 0.8052 (t0) cc_final: 0.7674 (m-40) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 0.2367 time to fit residues: 24.5186 Evaluate side-chains 89 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 32 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3121 Z= 0.131 Angle : 0.524 9.756 4205 Z= 0.254 Chirality : 0.035 0.118 505 Planarity : 0.003 0.033 540 Dihedral : 3.631 17.279 423 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.92 % Allowed : 23.39 % Favored : 73.68 % 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 (0.45), residues: 380 helix: 0.89 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.86 (0.57), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 91 HIS 0.001 0.000 HIS D 138 PHE 0.006 0.001 PHE D 156 TYR 0.007 0.001 TYR B 95 ARG 0.005 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.349 Fit side-chains REVERT: B 24 SER cc_start: 0.8681 (m) cc_final: 0.8298 (p) REVERT: B 66 ARG cc_start: 0.7215 (mtm180) cc_final: 0.6872 (mtm-85) REVERT: B 114 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.5772 (p90) REVERT: D 172 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7918 (t-90) REVERT: A 41 MET cc_start: 0.8736 (tpt) cc_final: 0.8183 (tpp) REVERT: A 49 ARG cc_start: 0.7494 (mtt180) cc_final: 0.5952 (mmt180) REVERT: A 52 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7504 (mm-30) REVERT: C 30 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6550 (tp30) REVERT: C 36 ASN cc_start: 0.8096 (t0) cc_final: 0.7745 (m-40) REVERT: C 69 LYS cc_start: 0.8370 (mtpt) cc_final: 0.8086 (tppt) outliers start: 10 outliers final: 6 residues processed: 86 average time/residue: 0.2620 time to fit residues: 25.2269 Evaluate side-chains 84 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3121 Z= 0.206 Angle : 0.567 7.514 4205 Z= 0.280 Chirality : 0.038 0.116 505 Planarity : 0.004 0.036 540 Dihedral : 3.867 17.000 423 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.51 % Allowed : 22.81 % Favored : 73.68 % 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: 0.20 (0.44), residues: 380 helix: 0.89 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.91 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 91 HIS 0.001 0.000 HIS D 138 PHE 0.009 0.001 PHE B 52 TYR 0.011 0.001 TYR B 95 ARG 0.005 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.369 Fit side-chains REVERT: B 114 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.5952 (p90) REVERT: D 170 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7311 (tp) REVERT: D 172 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.7917 (t-90) REVERT: A 41 MET cc_start: 0.8709 (tpt) cc_final: 0.8135 (tpp) REVERT: A 49 ARG cc_start: 0.7794 (mtt180) cc_final: 0.6169 (mmt180) REVERT: A 52 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7516 (mm-30) REVERT: C 30 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6866 (tp30) REVERT: C 36 ASN cc_start: 0.8032 (t0) cc_final: 0.7654 (m-40) REVERT: C 69 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8120 (tppt) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 0.2362 time to fit residues: 22.3279 Evaluate side-chains 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.0030 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.4728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 84 GLN D 29 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3121 Z= 0.131 Angle : 0.536 9.822 4205 Z= 0.257 Chirality : 0.035 0.118 505 Planarity : 0.003 0.035 540 Dihedral : 3.570 16.612 423 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.92 % Allowed : 24.56 % Favored : 72.51 % 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: 0.61 (0.45), residues: 380 helix: 1.21 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.80 (0.57), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 91 HIS 0.001 0.000 HIS B 78 PHE 0.007 0.001 PHE D 133 TYR 0.008 0.001 TYR B 95 ARG 0.005 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.362 Fit side-chains REVERT: B 66 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6869 (mtm-85) REVERT: B 114 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.5920 (p90) REVERT: D 172 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7916 (t-90) REVERT: A 49 ARG cc_start: 0.7626 (mtt180) cc_final: 0.6101 (mmt180) REVERT: C 30 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6892 (tp30) REVERT: C 36 ASN cc_start: 0.8118 (t0) cc_final: 0.7750 (m-40) outliers start: 10 outliers final: 6 residues processed: 82 average time/residue: 0.2610 time to fit residues: 24.1576 Evaluate side-chains 81 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.0020 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3121 Z= 0.154 Angle : 0.548 6.710 4205 Z= 0.266 Chirality : 0.035 0.119 505 Planarity : 0.003 0.036 540 Dihedral : 3.541 16.416 423 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.63 % Allowed : 24.85 % Favored : 72.51 % 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: 0.77 (0.45), residues: 380 helix: 1.34 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.77 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 91 HIS 0.001 0.000 HIS D 138 PHE 0.006 0.001 PHE B 52 TYR 0.009 0.001 TYR B 95 ARG 0.005 0.000 ARG D 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.328 Fit side-chains REVERT: B 24 SER cc_start: 0.8667 (m) cc_final: 0.8323 (p) REVERT: B 66 ARG cc_start: 0.7242 (mtm180) cc_final: 0.6893 (mtm-85) REVERT: B 114 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6096 (p90) REVERT: D 172 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7850 (t-90) REVERT: A 49 ARG cc_start: 0.7564 (mtt180) cc_final: 0.6078 (mmt180) REVERT: C 30 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6851 (tp30) REVERT: C 36 ASN cc_start: 0.8123 (t0) cc_final: 0.7750 (m-40) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 0.2584 time to fit residues: 23.1980 Evaluate side-chains 81 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.0170 chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 14 optimal weight: 6.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.169468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138388 restraints weight = 4120.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138656 restraints weight = 3619.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139168 restraints weight = 3182.949| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3121 Z= 0.129 Angle : 0.532 9.775 4205 Z= 0.254 Chirality : 0.035 0.119 505 Planarity : 0.003 0.032 540 Dihedral : 3.379 16.700 423 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.05 % Allowed : 26.02 % Favored : 71.93 % 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: 1.12 (0.45), residues: 380 helix: 1.54 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.48 (0.58), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 91 HIS 0.001 0.000 HIS B 78 PHE 0.006 0.000 PHE D 133 TYR 0.007 0.001 TYR B 95 ARG 0.005 0.000 ARG D 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1274.29 seconds wall clock time: 23 minutes 15.16 seconds (1395.16 seconds total)