Starting phenix.real_space_refine on Wed Mar 5 17:17:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x0u_21984/03_2025/6x0u_21984.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x0u_21984/03_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_21984/03_2025/6x0u_21984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x0u_21984/03_2025/6x0u_21984.map" model { file = "/net/cci-nas-00/data/ceres_data/6x0u_21984/03_2025/6x0u_21984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x0u_21984/03_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-5624/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: 3.42, per 1000 atoms: 1.11 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: 0.71 Conformation dependent library (CDL) restraints added in 372.3 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: 0.41 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: 0.73 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: 2.030 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.530 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: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.830 ------------------------------------------------------------------------------- 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 : 0.376 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: 0.2614 time to fit residues: 33.4288 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 : 0.315 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 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: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.164678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136321 restraints weight = 4275.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134009 restraints weight = 6363.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134471 restraints weight = 6461.278| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3121 Z= 0.247 Angle : 0.646 7.997 4205 Z= 0.324 Chirality : 0.039 0.136 505 Planarity : 0.005 0.040 540 Dihedral : 4.677 17.862 423 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.46 % Allowed : 16.96 % Favored : 81.58 % 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: -4.08 (0.35), residues: 380 helix: -2.59 (0.24), residues: 277 sheet: None (None), residues: 0 loop : -2.36 (0.57), residues: 103 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 0.001 PHE D 133 TYR 0.010 0.002 TYR B 95 ARG 0.005 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 97 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.365 Fit side-chains REVERT: B 66 ARG cc_start: 0.7147 (mtm180) cc_final: 0.6851 (mtm-85) REVERT: B 88 LYS cc_start: 0.8022 (tppt) cc_final: 0.7653 (tttp) REVERT: B 114 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6210 (p90) REVERT: D 42 TYR cc_start: 0.7849 (m-80) cc_final: 0.7184 (m-80) REVERT: D 95 GLU cc_start: 0.7660 (tt0) cc_final: 0.7428 (tt0) REVERT: D 167 GLU cc_start: 0.8425 (mp0) cc_final: 0.7504 (pt0) REVERT: A 41 MET cc_start: 0.8754 (tpt) cc_final: 0.8436 (tpp) REVERT: C 58 GLU cc_start: 0.7215 (mp0) cc_final: 0.6790 (mp0) REVERT: C 67 LEU cc_start: 0.8302 (mm) cc_final: 0.7931 (mt) outliers start: 5 outliers final: 3 residues processed: 95 average time/residue: 0.2238 time to fit residues: 24.1753 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 : 0.361 ------------------------------------------------------------------------------- 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: 0.0770 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.5340 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.167533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138999 restraints weight = 4250.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136671 restraints weight = 5174.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137631 restraints weight = 6028.024| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3121 Z= 0.141 Angle : 0.542 7.341 4205 Z= 0.270 Chirality : 0.035 0.121 505 Planarity : 0.003 0.036 540 Dihedral : 4.104 18.509 423 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.92 % Allowed : 21.05 % 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: -2.10 (0.41), residues: 380 helix: -0.96 (0.30), residues: 269 sheet: None (None), residues: 0 loop : -2.15 (0.56), 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 0.008 0.001 TYR B 95 ARG 0.003 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 99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.325 Fit side-chains REVERT: B 24 SER cc_start: 0.8298 (m) cc_final: 0.7854 (p) REVERT: B 66 ARG cc_start: 0.7188 (mtm180) cc_final: 0.6868 (mtm-85) REVERT: B 88 LYS cc_start: 0.8058 (tppt) cc_final: 0.7653 (tttp) REVERT: B 114 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.5431 (p90) REVERT: D 35 ARG cc_start: 0.6383 (tpt170) cc_final: 0.6151 (tpt170) REVERT: D 95 GLU cc_start: 0.7772 (tt0) cc_final: 0.7567 (tt0) REVERT: A 41 MET cc_start: 0.8633 (tpt) cc_final: 0.8375 (tpp) REVERT: A 49 ARG cc_start: 0.7518 (mtt180) cc_final: 0.6121 (mmt180) REVERT: C 36 ASN cc_start: 0.8139 (t0) cc_final: 0.7708 (t0) REVERT: C 67 LEU cc_start: 0.8258 (mm) cc_final: 0.7914 (mt) outliers start: 10 outliers final: 4 residues processed: 94 average time/residue: 0.2498 time to fit residues: 26.3844 Evaluate side-chains 87 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 172 HIS Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.0000 chunk 9 optimal weight: 0.8980 overall best weight: 0.5282 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.166341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 142)---------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136738 restraints weight = 4170.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 89)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135377 restraints weight = 5428.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135996 restraints weight = 4435.907| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3121 Z= 0.133 Angle : 0.535 9.175 4205 Z= 0.261 Chirality : 0.035 0.120 505 Planarity : 0.003 0.032 540 Dihedral : 3.862 17.742 423 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.09 % Allowed : 20.76 % 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: -1.12 (0.43), residues: 380 helix: -0.20 (0.32), residues: 275 sheet: None (None), residues: 0 loop : -1.96 (0.57), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 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 37 *********************** 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: 14 poor density : 84 time to evaluate : 0.365 Fit side-chains REVERT: B 19 ARG cc_start: 0.7949 (mmm160) cc_final: 0.7714 (mmm160) REVERT: B 23 ARG cc_start: 0.6186 (mmt90) cc_final: 0.5807 (mmt90) REVERT: B 66 ARG cc_start: 0.7103 (mtm180) cc_final: 0.6810 (mtm-85) REVERT: B 84 GLN cc_start: 0.8070 (mt0) cc_final: 0.7844 (mt0) REVERT: B 88 LYS cc_start: 0.8040 (tppt) cc_final: 0.7655 (tttp) REVERT: B 114 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.5615 (p90) REVERT: A 41 MET cc_start: 0.8504 (tpt) cc_final: 0.8291 (tpp) REVERT: A 49 ARG cc_start: 0.7338 (mtt180) cc_final: 0.5972 (mmt180) REVERT: C 36 ASN cc_start: 0.8158 (t0) cc_final: 0.7725 (m-40) REVERT: C 67 LEU cc_start: 0.8136 (mm) cc_final: 0.7744 (mt) outliers start: 14 outliers final: 9 residues processed: 92 average time/residue: 0.2533 time to fit residues: 26.1522 Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.0370 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.168416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136206 restraints weight = 4102.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137079 restraints weight = 3438.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137337 restraints weight = 3026.214| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3121 Z= 0.159 Angle : 0.537 7.596 4205 Z= 0.264 Chirality : 0.036 0.118 505 Planarity : 0.003 0.032 540 Dihedral : 3.825 17.469 423 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.80 % Allowed : 21.35 % 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: -0.72 (0.44), residues: 380 helix: 0.16 (0.33), residues: 276 sheet: None (None), residues: 0 loop : -2.03 (0.56), residues: 104 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 8 TYR 0.010 0.001 TYR B 95 ARG 0.003 0.000 ARG D 88 *********************** 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: 13 poor density : 81 time to evaluate : 0.376 Fit side-chains REVERT: B 66 ARG cc_start: 0.7175 (mtm180) cc_final: 0.6851 (mtm-85) REVERT: B 88 LYS cc_start: 0.8090 (tppt) cc_final: 0.7770 (tttp) REVERT: B 114 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.5600 (p90) REVERT: D 135 ASN cc_start: 0.6624 (OUTLIER) cc_final: 0.6296 (p0) REVERT: D 172 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7732 (t-90) REVERT: A 41 MET cc_start: 0.8646 (tpt) cc_final: 0.8203 (tpp) REVERT: A 49 ARG cc_start: 0.7408 (mtt180) cc_final: 0.6032 (mmt180) REVERT: C 30 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6243 (tp30) REVERT: C 36 ASN cc_start: 0.8077 (t0) cc_final: 0.7718 (m-40) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 0.2557 time to fit residues: 25.5326 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 : 0.334 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 0.0670 chunk 22 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.169980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142999 restraints weight = 4174.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141227 restraints weight = 6309.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141917 restraints weight = 5914.176| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3121 Z= 0.131 Angle : 0.508 6.811 4205 Z= 0.249 Chirality : 0.035 0.118 505 Planarity : 0.003 0.033 540 Dihedral : 3.661 17.590 423 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.22 % Allowed : 21.93 % 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: -0.15 (0.44), residues: 380 helix: 0.59 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.89 (0.58), 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 0.009 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 93 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.368 Fit side-chains REVERT: B 66 ARG cc_start: 0.7198 (mtm180) cc_final: 0.6850 (mtm-85) REVERT: B 88 LYS cc_start: 0.8057 (tppt) cc_final: 0.7697 (tttp) REVERT: B 114 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.5570 (p90) REVERT: D 135 ASN cc_start: 0.6538 (OUTLIER) cc_final: 0.6224 (p0) REVERT: D 172 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7819 (t-90) REVERT: A 41 MET cc_start: 0.8615 (tpt) cc_final: 0.8126 (tpp) REVERT: A 49 ARG cc_start: 0.7139 (mtt180) cc_final: 0.5949 (mmt180) REVERT: C 30 GLU cc_start: 0.6335 (mm-30) cc_final: 0.6093 (tp30) REVERT: C 36 ASN cc_start: 0.8125 (t0) cc_final: 0.7736 (m-40) outliers start: 11 outliers final: 6 residues processed: 89 average time/residue: 0.2668 time to fit residues: 26.6374 Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 5.9990 chunk 3 optimal weight: 0.0060 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 18 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.170980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139175 restraints weight = 4089.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140043 restraints weight = 3380.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140705 restraints weight = 2958.197| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3121 Z= 0.133 Angle : 0.543 9.807 4205 Z= 0.255 Chirality : 0.035 0.118 505 Planarity : 0.003 0.033 540 Dihedral : 3.510 17.511 423 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.92 % Allowed : 22.22 % 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: 0.36 (0.45), residues: 380 helix: 0.95 (0.33), residues: 276 sheet: None (None), residues: 0 loop : -1.63 (0.60), residues: 104 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 0.006 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: 10 poor density : 79 time to evaluate : 0.366 Fit side-chains REVERT: B 66 ARG cc_start: 0.7171 (mtm180) cc_final: 0.6856 (mtm-85) REVERT: B 84 GLN cc_start: 0.8023 (mt0) cc_final: 0.7822 (mt0) REVERT: B 88 LYS cc_start: 0.8140 (tppt) cc_final: 0.7729 (tttp) REVERT: B 114 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.5647 (p90) REVERT: D 172 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7822 (t-90) REVERT: A 41 MET cc_start: 0.8617 (tpt) cc_final: 0.8076 (tpp) REVERT: A 49 ARG cc_start: 0.7135 (mtt180) cc_final: 0.5947 (mmt180) REVERT: C 30 GLU cc_start: 0.6583 (mm-30) cc_final: 0.6328 (tp30) REVERT: C 36 ASN cc_start: 0.8132 (t0) cc_final: 0.7800 (m-40) outliers start: 10 outliers final: 4 residues processed: 85 average time/residue: 0.2571 time to fit residues: 24.5491 Evaluate side-chains 80 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.0010 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.0070 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143034 restraints weight = 4102.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138087 restraints weight = 5125.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.139091 restraints weight = 4051.234| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4980 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= 0.134 Angle : 0.523 7.329 4205 Z= 0.251 Chirality : 0.035 0.117 505 Planarity : 0.003 0.032 540 Dihedral : 3.436 17.803 423 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.05 % Allowed : 21.93 % 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: 0.63 (0.45), residues: 380 helix: 1.19 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.66 (0.59), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 91 HIS 0.001 0.000 HIS D 138 PHE 0.006 0.001 PHE D 133 TYR 0.008 0.001 TYR B 95 ARG 0.002 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 84 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.372 Fit side-chains REVERT: B 66 ARG cc_start: 0.7169 (mtm180) cc_final: 0.6833 (mtm-85) REVERT: B 88 LYS cc_start: 0.8136 (tppt) cc_final: 0.7733 (tttp) REVERT: B 114 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.5663 (p90) REVERT: D 172 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7833 (t-90) REVERT: A 41 MET cc_start: 0.8585 (tpt) cc_final: 0.8039 (tpp) REVERT: A 49 ARG cc_start: 0.7085 (mtt180) cc_final: 0.5913 (mmt180) REVERT: C 30 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6449 (tp30) REVERT: C 36 ASN cc_start: 0.8142 (t0) cc_final: 0.7819 (m-40) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.2437 time to fit residues: 22.4786 Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 TYR 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 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.165645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138135 restraints weight = 4193.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135859 restraints weight = 6177.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136700 restraints weight = 5787.855| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 0.027 3121 Z= 0.158 Angle : 0.568 10.190 4205 Z= 0.266 Chirality : 0.036 0.116 505 Planarity : 0.003 0.033 540 Dihedral : 3.497 15.319 423 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.63 % Allowed : 20.76 % Favored : 76.61 % 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: 0.72 (0.45), residues: 380 helix: 1.26 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.69 (0.58), 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 0.007 0.001 PHE B 52 TYR 0.010 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 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.393 Fit side-chains REVERT: B 66 ARG cc_start: 0.7241 (mtm180) cc_final: 0.6883 (mtm-85) REVERT: B 114 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.5895 (p90) REVERT: D 172 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7853 (t-90) REVERT: A 41 MET cc_start: 0.8560 (tpt) cc_final: 0.8033 (tpp) REVERT: A 49 ARG cc_start: 0.7097 (mtt180) cc_final: 0.5991 (mmt180) REVERT: C 36 ASN cc_start: 0.8132 (t0) cc_final: 0.7725 (m-40) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 0.2627 time to fit residues: 23.6764 Evaluate side-chains 78 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 20 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.163786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136457 restraints weight = 4142.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133542 restraints weight = 6275.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134531 restraints weight = 6311.019| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5028 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= 0.186 Angle : 0.579 8.277 4205 Z= 0.273 Chirality : 0.037 0.115 505 Planarity : 0.004 0.034 540 Dihedral : 3.671 15.730 423 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.34 % Allowed : 20.76 % Favored : 76.90 % 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: 0.69 (0.44), residues: 380 helix: 1.24 (0.32), residues: 277 sheet: None (None), residues: 0 loop : -1.68 (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 0.008 0.001 PHE D 8 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 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.339 Fit side-chains REVERT: B 66 ARG cc_start: 0.7299 (mtm180) cc_final: 0.6926 (mtm-85) REVERT: B 114 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.5958 (p90) REVERT: D 172 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7814 (t-90) REVERT: A 41 MET cc_start: 0.8627 (tpt) cc_final: 0.8078 (tpp) REVERT: A 49 ARG cc_start: 0.7348 (mtt180) cc_final: 0.5979 (mmt180) REVERT: C 36 ASN cc_start: 0.8121 (t0) cc_final: 0.7698 (m-40) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.2501 time to fit residues: 22.4640 Evaluate side-chains 80 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.0050 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.165753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138758 restraints weight = 4209.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.135802 restraints weight = 6190.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136930 restraints weight = 6085.660| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3121 Z= 0.158 Angle : 0.583 9.939 4205 Z= 0.270 Chirality : 0.035 0.115 505 Planarity : 0.003 0.033 540 Dihedral : 3.540 15.761 423 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.63 % Allowed : 20.76 % Favored : 76.61 % 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: 0.88 (0.45), residues: 380 helix: 1.40 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.66 (0.58), residues: 103 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 0.006 0.001 PHE D 8 TYR 0.009 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: 1709.46 seconds wall clock time: 30 minutes 3.83 seconds (1803.83 seconds total)