Starting phenix.real_space_refine on Mon Feb 10 22:19:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x0u_21984/02_2025/6x0u_21984.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x0u_21984/02_2025/6x0u_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/cci-nas-00/data/ceres_data/6x0u_21984/02_2025/6x0u_21984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x0u_21984/02_2025/6x0u_21984.map" model { file = "/net/cci-nas-00/data/ceres_data/6x0u_21984/02_2025/6x0u_21984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x0u_21984/02_2025/6x0u_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-5592/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: 3.11, per 1000 atoms: 1.01 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: 0.76 Conformation dependent library (CDL) restraints added in 365.6 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: 0.64 Time building geometry restraints manager: 0.86 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.580 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.383 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: 0.2713 time to fit residues: 34.6016 Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136289 restraints weight = 4282.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133911 restraints weight = 5322.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134752 restraints weight = 5787.380| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.377 Fit side-chains REVERT: B 23 ARG cc_start: 0.6150 (mmt90) cc_final: 0.5947 (mmt90) REVERT: B 66 ARG cc_start: 0.7186 (mtm180) cc_final: 0.6880 (mtm-85) REVERT: B 88 LYS cc_start: 0.8083 (tppt) cc_final: 0.7703 (tttp) REVERT: B 114 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6142 (p90) REVERT: D 42 TYR cc_start: 0.7802 (m-80) cc_final: 0.7173 (m-80) REVERT: D 95 GLU cc_start: 0.7710 (tt0) cc_final: 0.7496 (tt0) REVERT: D 167 GLU cc_start: 0.8489 (mp0) cc_final: 0.7516 (pt0) REVERT: A 41 MET cc_start: 0.8755 (tpt) cc_final: 0.8415 (tpp) REVERT: C 58 GLU cc_start: 0.7255 (mp0) cc_final: 0.6720 (mp0) REVERT: C 67 LEU cc_start: 0.8332 (mm) cc_final: 0.7927 (mt) outliers start: 5 outliers final: 3 residues processed: 95 average time/residue: 0.2227 time to fit residues: 24.0632 Evaluate side-chains 84 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.0070 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.167463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139374 restraints weight = 4214.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137478 restraints weight = 6324.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138430 restraints weight = 6070.346| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4008 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= 0.136 Angle : 0.531 7.144 4205 Z= 0.266 Chirality : 0.035 0.121 505 Planarity : 0.003 0.034 540 Dihedral : 4.103 18.594 423 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.51 % Allowed : 21.05 % Favored : 75.44 % 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: -1.97 (0.41), residues: 380 helix: -0.90 (0.30), residues: 269 sheet: None (None), residues: 0 loop : -2.01 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 91 HIS 0.001 0.000 HIS B 78 PHE 0.006 0.001 PHE D 133 TYR 0.007 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 100 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.413 Fit side-chains REVERT: B 66 ARG cc_start: 0.7251 (mtm180) cc_final: 0.6911 (mtm-85) REVERT: B 88 LYS cc_start: 0.8075 (tppt) cc_final: 0.7717 (tttp) REVERT: B 114 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.5598 (p90) REVERT: D 35 ARG cc_start: 0.6349 (tpt170) cc_final: 0.6120 (tpt170) REVERT: D 95 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: D 134 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7399 (mt) REVERT: A 41 MET cc_start: 0.8647 (tpt) cc_final: 0.8347 (tpp) REVERT: A 49 ARG cc_start: 0.7463 (mtt180) cc_final: 0.6235 (mmt180) REVERT: C 36 ASN cc_start: 0.8156 (t0) cc_final: 0.7705 (t0) outliers start: 12 outliers final: 3 residues processed: 94 average time/residue: 0.2502 time to fit residues: 26.4676 Evaluate side-chains 91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 95 GLU 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 12 optimal weight: 0.2980 chunk 7 optimal weight: 0.0470 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.167054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137063 restraints weight = 4154.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135331 restraints weight = 6353.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137016 restraints weight = 5415.573| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3121 Z= 0.131 Angle : 0.522 9.286 4205 Z= 0.255 Chirality : 0.034 0.121 505 Planarity : 0.003 0.030 540 Dihedral : 3.769 17.432 423 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.51 % Allowed : 21.93 % Favored : 74.56 % 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: -1.00 (0.43), residues: 380 helix: -0.10 (0.32), residues: 272 sheet: None (None), residues: 0 loop : -1.91 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 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 0.004 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 98 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.342 Fit side-chains REVERT: B 23 ARG cc_start: 0.6141 (mmt90) cc_final: 0.5657 (mmt90) REVERT: B 50 ASP cc_start: 0.7678 (p0) cc_final: 0.7426 (p0) REVERT: B 66 ARG cc_start: 0.7216 (mtm180) cc_final: 0.6870 (mtm-85) REVERT: B 84 GLN cc_start: 0.8099 (mt0) cc_final: 0.7866 (mt0) REVERT: B 114 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.5635 (p90) REVERT: D 172 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7626 (t-90) REVERT: A 41 MET cc_start: 0.8495 (tpt) cc_final: 0.8266 (tpp) REVERT: A 49 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6007 (mmt180) REVERT: C 36 ASN cc_start: 0.8171 (t0) cc_final: 0.7705 (m-40) REVERT: C 67 LEU cc_start: 0.8138 (mm) cc_final: 0.7736 (mt) outliers start: 12 outliers final: 8 residues processed: 92 average time/residue: 0.2473 time to fit residues: 25.5533 Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 73 LEU 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 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 9 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.0570 chunk 36 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.168001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137609 restraints weight = 4128.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135232 restraints weight = 6815.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137192 restraints weight = 5911.959| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4573 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 : 0.510 7.748 4205 Z= 0.250 Chirality : 0.034 0.120 505 Planarity : 0.003 0.029 540 Dihedral : 3.592 17.516 423 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.51 % Allowed : 21.93 % Favored : 74.56 % 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: -0.48 (0.44), residues: 380 helix: 0.32 (0.32), residues: 279 sheet: None (None), residues: 0 loop : -1.95 (0.58), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 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 0.004 0.000 ARG B 19 *********************** 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 94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.372 Fit side-chains REVERT: B 19 ARG cc_start: 0.7948 (mmm160) cc_final: 0.7618 (mmm160) REVERT: B 66 ARG cc_start: 0.7161 (mtm180) cc_final: 0.6830 (mtm-85) REVERT: B 114 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.5628 (p90) REVERT: D 134 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7138 (pp) REVERT: D 172 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7709 (t-90) REVERT: A 41 MET cc_start: 0.8574 (tpt) cc_final: 0.8112 (tpp) REVERT: A 49 ARG cc_start: 0.7159 (mtt180) cc_final: 0.5895 (mmt180) REVERT: C 30 GLU cc_start: 0.6369 (mm-30) cc_final: 0.6105 (tp30) REVERT: C 36 ASN cc_start: 0.8105 (t0) cc_final: 0.7685 (m-40) REVERT: C 67 LEU cc_start: 0.8146 (mm) cc_final: 0.7672 (mt) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.2600 time to fit residues: 26.1918 Evaluate side-chains 83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 134 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3885 r_free = 0.3885 target = 0.162828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133970 restraints weight = 4213.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131953 restraints weight = 7303.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132679 restraints weight = 6518.147| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3121 Z= 0.197 Angle : 0.570 9.340 4205 Z= 0.277 Chirality : 0.037 0.116 505 Planarity : 0.003 0.031 540 Dihedral : 3.867 16.771 423 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.09 % Allowed : 21.05 % Favored : 74.85 % 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: -0.28 (0.44), residues: 380 helix: 0.48 (0.32), residues: 282 sheet: None (None), residues: 0 loop : -2.00 (0.57), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 91 HIS 0.001 0.000 HIS D 138 PHE 0.008 0.001 PHE B 52 TYR 0.011 0.001 TYR B 95 ARG 0.003 0.000 ARG B 19 *********************** 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 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.371 Fit side-chains REVERT: B 66 ARG cc_start: 0.7274 (mtm180) cc_final: 0.6910 (mtm-85) REVERT: B 114 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6064 (p90) REVERT: D 135 ASN cc_start: 0.6561 (m-40) cc_final: 0.6298 (p0) REVERT: D 172 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7774 (t-90) REVERT: A 41 MET cc_start: 0.8702 (tpt) cc_final: 0.8202 (tpp) REVERT: A 49 ARG cc_start: 0.7605 (mtt180) cc_final: 0.6391 (mmt180) REVERT: C 30 GLU cc_start: 0.6376 (mm-30) cc_final: 0.6121 (tp30) REVERT: C 36 ASN cc_start: 0.8153 (t0) cc_final: 0.7757 (m-40) outliers start: 14 outliers final: 6 residues processed: 84 average time/residue: 0.2516 time to fit residues: 23.8326 Evaluate side-chains 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 7.9990 chunk 3 optimal weight: 0.0470 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.169384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140923 restraints weight = 4088.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138545 restraints weight = 5897.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139422 restraints weight = 5865.701| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4833 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= 0.144 Angle : 0.550 8.644 4205 Z= 0.263 Chirality : 0.035 0.116 505 Planarity : 0.003 0.031 540 Dihedral : 3.648 17.646 423 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.51 % Allowed : 21.64 % Favored : 74.85 % 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: 0.14 (0.44), residues: 380 helix: 0.84 (0.33), residues: 279 sheet: None (None), residues: 0 loop : -1.96 (0.55), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 91 HIS 0.001 0.000 HIS D 138 PHE 0.005 0.001 PHE D 133 TYR 0.008 0.001 TYR B 95 ARG 0.003 0.000 ARG B 37 *********************** 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 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.380 Fit side-chains REVERT: B 66 ARG cc_start: 0.7266 (mtm180) cc_final: 0.6896 (mtm-85) REVERT: B 114 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6016 (p90) REVERT: D 172 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7839 (t-90) REVERT: A 41 MET cc_start: 0.8649 (tpt) cc_final: 0.8096 (tpp) REVERT: A 49 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6083 (mmt180) REVERT: C 30 GLU cc_start: 0.6328 (mm-30) cc_final: 0.6112 (tp30) REVERT: C 36 ASN cc_start: 0.8126 (t0) cc_final: 0.7732 (m-40) outliers start: 12 outliers final: 5 residues processed: 85 average time/residue: 0.2409 time to fit residues: 23.0567 Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.166000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 166)---------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136266 restraints weight = 4149.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131019 restraints weight = 6090.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132163 restraints weight = 4813.084| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5006 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= 0.153 Angle : 0.565 9.651 4205 Z= 0.268 Chirality : 0.036 0.117 505 Planarity : 0.003 0.032 540 Dihedral : 3.611 17.118 423 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.34 % Allowed : 22.81 % Favored : 74.85 % 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: 0.38 (0.44), residues: 380 helix: 1.03 (0.33), residues: 279 sheet: None (None), residues: 0 loop : -1.91 (0.56), residues: 101 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 0.003 0.000 ARG B 37 *********************** 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 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.350 Fit side-chains REVERT: B 66 ARG cc_start: 0.7176 (mtm180) cc_final: 0.6839 (mtm-85) REVERT: B 114 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6136 (p90) REVERT: D 172 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7816 (t-90) REVERT: A 41 MET cc_start: 0.8672 (tpt) cc_final: 0.8067 (tpp) REVERT: A 49 ARG cc_start: 0.7480 (mtt180) cc_final: 0.6195 (mmt180) REVERT: C 30 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6660 (tp30) REVERT: C 36 ASN cc_start: 0.8140 (t0) cc_final: 0.7774 (m-40) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.2721 time to fit residues: 24.0477 Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 36 ASN 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 21 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.168313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138921 restraints weight = 4158.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137549 restraints weight = 6130.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137763 restraints weight = 5976.829| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3121 Z= 0.147 Angle : 0.567 9.370 4205 Z= 0.267 Chirality : 0.035 0.118 505 Planarity : 0.003 0.032 540 Dihedral : 3.503 16.349 423 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.63 % Allowed : 21.64 % Favored : 75.73 % 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: 0.67 (0.45), residues: 380 helix: 1.25 (0.33), residues: 279 sheet: None (None), residues: 0 loop : -1.83 (0.57), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 91 HIS 0.001 0.000 HIS B 78 PHE 0.007 0.001 PHE D 133 TYR 0.009 0.001 TYR B 95 ARG 0.004 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 84 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.345 Fit side-chains REVERT: B 66 ARG cc_start: 0.7112 (mtm180) cc_final: 0.6815 (mtm-85) REVERT: B 114 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6236 (p90) REVERT: D 172 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7793 (t-90) REVERT: A 41 MET cc_start: 0.8578 (tpt) cc_final: 0.8016 (tpp) REVERT: A 49 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6076 (mmt180) REVERT: C 36 ASN cc_start: 0.8134 (t0) cc_final: 0.7728 (m-40) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.2505 time to fit residues: 23.1719 Evaluate side-chains 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 36 ASN 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 18 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.0170 chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.163178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135900 restraints weight = 4139.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133191 restraints weight = 5517.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134135 restraints weight = 5325.406| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5109 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= 0.191 Angle : 0.577 8.444 4205 Z= 0.276 Chirality : 0.037 0.115 505 Planarity : 0.004 0.034 540 Dihedral : 3.729 15.813 423 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.34 % Allowed : 22.22 % Favored : 75.44 % 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: 0.64 (0.44), residues: 380 helix: 1.17 (0.32), residues: 279 sheet: None (None), residues: 0 loop : -1.66 (0.58), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 91 HIS 0.002 0.000 HIS D 138 PHE 0.008 0.001 PHE B 52 TYR 0.011 0.001 TYR B 95 ARG 0.006 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 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.353 Fit side-chains REVERT: B 114 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6550 (p90) REVERT: D 95 GLU cc_start: 0.7369 (tt0) cc_final: 0.7151 (tt0) REVERT: D 172 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7767 (t-90) REVERT: A 41 MET cc_start: 0.8637 (tpt) cc_final: 0.8082 (tpp) REVERT: A 49 ARG cc_start: 0.7575 (mtt180) cc_final: 0.6341 (mmt180) REVERT: C 36 ASN cc_start: 0.8147 (t0) cc_final: 0.7723 (m-40) outliers start: 8 outliers final: 6 residues processed: 78 average time/residue: 0.2366 time to fit residues: 21.0581 Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 36 ASN 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6442 > 50: distance: 1 - 18: 19.465 distance: 9 - 33: 20.908 distance: 12 - 18: 19.525 distance: 13 - 38: 18.948 distance: 18 - 19: 16.537 distance: 19 - 20: 15.133 distance: 19 - 22: 32.798 distance: 20 - 21: 28.474 distance: 20 - 24: 6.742 distance: 22 - 23: 42.864 distance: 24 - 25: 13.506 distance: 25 - 26: 12.938 distance: 25 - 28: 12.576 distance: 26 - 27: 32.004 distance: 26 - 33: 15.346 distance: 28 - 29: 13.622 distance: 29 - 30: 4.798 distance: 30 - 31: 12.702 distance: 30 - 32: 9.865 distance: 33 - 34: 21.077 distance: 34 - 35: 11.673 distance: 34 - 37: 14.251 distance: 35 - 36: 22.091 distance: 35 - 38: 10.916 distance: 38 - 39: 12.188 distance: 39 - 40: 16.071 distance: 39 - 42: 24.025 distance: 40 - 41: 30.457 distance: 40 - 46: 30.318 distance: 42 - 43: 12.346 distance: 43 - 44: 21.743 distance: 43 - 45: 21.542 distance: 46 - 47: 11.861 distance: 47 - 48: 21.615 distance: 47 - 50: 13.236 distance: 48 - 49: 30.163 distance: 48 - 54: 19.268 distance: 50 - 51: 8.089 distance: 51 - 52: 18.552 distance: 51 - 53: 18.618 distance: 54 - 55: 20.029 distance: 54 - 60: 10.596 distance: 55 - 56: 18.141 distance: 55 - 58: 16.555 distance: 56 - 57: 30.104 distance: 56 - 61: 22.641 distance: 58 - 59: 38.689 distance: 59 - 60: 19.610 distance: 61 - 62: 15.172 distance: 62 - 63: 20.297 distance: 62 - 65: 20.459 distance: 63 - 64: 9.739 distance: 63 - 66: 7.230 distance: 66 - 67: 8.913 distance: 67 - 68: 7.797 distance: 67 - 70: 17.483 distance: 68 - 69: 8.149 distance: 71 - 72: 4.532 distance: 72 - 73: 6.942 distance: 72 - 75: 4.773 distance: 73 - 74: 6.496 distance: 75 - 76: 5.774 distance: 79 - 80: 12.372 distance: 80 - 81: 9.943 distance: 80 - 83: 20.957 distance: 81 - 82: 29.712 distance: 81 - 90: 18.694 distance: 83 - 84: 15.356 distance: 84 - 85: 10.629 distance: 85 - 86: 5.554 distance: 86 - 87: 6.609 distance: 87 - 88: 12.808 distance: 87 - 89: 8.279