Starting phenix.real_space_refine on Thu Sep 10 23:33:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6yw7_10960/09_2026/6yw7_10960.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yw7_10960/09_2026/6yw7_10960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yw7_10960/09_2026/6yw7_10960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yw7_10960/09_2026/6yw7_10960.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6yw7_10960/09_2026/6yw7_10960.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6yw7_10960/09_2026/6yw7_10960.cif" model { file = "/net/cci-nas-00/data/ceres_data/6yw7_10960/09_2026/6yw7_10960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yw7_10960/09_2026/6yw7_10960.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 P 6 5.49 5 C 3596 2.51 5 N 1798 2.21 5 O 26 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5426 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 1188 Classifications: {'peptide': 396} Incomplete info: {'n_c_alpha_c_only': 396} Link IDs: {'PTRANS': 26, 'TRANS': 369} Chain breaks: 2 Unresolved chain link angles: 421 Unresolved non-hydrogen bonds: 2072 Unresolved non-hydrogen angles: 2818 Unresolved non-hydrogen dihedrals: 1103 Unresolved non-hydrogen chiralities: 481 Planarities with less than four sites: {'ARG:plan': 22, 'ASP:plan': 24, 'TYR:plan': 18, 'ASN:plan1': 10, 'GLU:plan': 32, 'GLN:plan1': 14, 'PHE:plan': 20, 'TRP:plan': 5, 'HIS:plan': 9} Unresolved non-hydrogen planarities: 818 Chain: "D" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 852 Classifications: {'peptide': 284} Incomplete info: {'n_c_alpha_c_only': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved chain link angles: 292 Unresolved non-hydrogen bonds: 1489 Unresolved non-hydrogen angles: 2017 Unresolved non-hydrogen dihedrals: 780 Unresolved non-hydrogen chiralities: 346 Planarities with less than four sites: {'GLU:plan': 21, 'ASN:plan1': 16, 'ARG:plan': 16, 'PHE:plan': 18, 'ASP:plan': 20, 'TYR:plan': 12, 'HIS:plan': 11, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 620 Chain: "E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 510 Classifications: {'peptide': 170} Incomplete info: {'n_c_alpha_c_only': 170} Link IDs: {'PTRANS': 11, 'TRANS': 158} Chain breaks: 1 Unresolved chain link angles: 180 Unresolved non-hydrogen bonds: 903 Unresolved non-hydrogen angles: 1215 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 202 Planarities with less than four sites: {'ASP:plan': 9, 'ASN:plan1': 10, 'ARG:plan': 7, 'GLN:plan1': 9, 'PHE:plan': 9, 'GLU:plan': 12, 'TYR:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 342 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 858 Classifications: {'peptide': 286} Incomplete info: {'n_c_alpha_c_only': 286} Link IDs: {'PTRANS': 14, 'TRANS': 271} Chain breaks: 3 Unresolved chain link angles: 299 Unresolved non-hydrogen bonds: 1467 Unresolved non-hydrogen angles: 1992 Unresolved non-hydrogen dihedrals: 764 Unresolved non-hydrogen chiralities: 353 Planarities with less than four sites: {'ASP:plan': 17, 'ASN:plan1': 7, 'PHE:plan': 14, 'TYR:plan': 12, 'GLU:plan': 20, 'HIS:plan': 8, 'TRP:plan': 2, 'GLN:plan1': 8, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 550 Chain: "F" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 495 Classifications: {'peptide': 165} Incomplete info: {'n_c_alpha_c_only': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Unresolved chain link angles: 168 Unresolved non-hydrogen bonds: 886 Unresolved non-hydrogen angles: 1190 Unresolved non-hydrogen dihedrals: 462 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'ARG:plan': 12, 'TYR:plan': 3, 'GLN:plan1': 5, 'GLU:plan': 19, 'ASN:plan1': 8, 'PHE:plan': 11, 'HIS:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 335 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 417 Classifications: {'peptide': 139} Incomplete info: {'n_c_alpha_c_only': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 1 Unresolved chain link angles: 142 Unresolved non-hydrogen bonds: 658 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 164 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 4, 'ASP:plan': 12, 'GLU:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 7, 'GLN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 230 Chain: "C" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 1044 Classifications: {'peptide': 348} Incomplete info: {'n_c_alpha_c_only': 348} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain breaks: 1 Unresolved chain link angles: 360 Unresolved non-hydrogen bonds: 1764 Unresolved non-hydrogen angles: 2409 Unresolved non-hydrogen dihedrals: 949 Unresolved non-hydrogen chiralities: 420 Planarities with less than four sites: {'HIS:plan': 13, 'GLN:plan1': 12, 'PHE:plan': 15, 'GLU:plan': 15, 'TRP:plan': 13, 'ASN:plan1': 14, 'ARG:plan': 13, 'ASP:plan': 19, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 666 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.73, per 1000 atoms: 0.32 Number of scatterers: 5426 At special positions: 0 Unit cell: (138.43, 91.56, 136.25, 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) P 6 15.00 O 26 8.00 N 1798 7.00 C 3596 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: 0.43 Conformation dependent library (CDL) restraints added in 504.6 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.27: 6 1.27 - 1.39: 1767 1.39 - 1.50: 2102 1.50 - 1.62: 1530 1.62 - 1.73: 10 Bond restraints: 5415 Sorted by residual: bond pdb=" C VAL A 83 " pdb=" N GLU A 84 " ideal model delta sigma weight residual 1.334 1.733 -0.398 1.27e-02 6.20e+03 9.84e+02 bond pdb=" C GLU A 280 " pdb=" N ILE A 281 " ideal model delta sigma weight residual 1.335 1.155 0.181 1.05e-02 9.07e+03 2.96e+02 bond pdb=" C ILE B 184 " pdb=" N ALA B 185 " ideal model delta sigma weight residual 1.331 1.535 -0.204 1.29e-02 6.01e+03 2.50e+02 bond pdb=" CA ALA B 261 " pdb=" C ALA B 261 " ideal model delta sigma weight residual 1.524 1.707 -0.183 1.26e-02 6.30e+03 2.11e+02 bond pdb=" C TYR B 310 " pdb=" N PRO B 311 " ideal model delta sigma weight residual 1.330 1.501 -0.171 1.19e-02 7.06e+03 2.07e+02 ... (remaining 5410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.20: 5360 12.20 - 24.40: 67 24.40 - 36.59: 10 36.59 - 48.79: 0 48.79 - 60.99: 1 Bond angle restraints: 5438 Sorted by residual: angle pdb=" CA GLN B 267 " pdb=" C GLN B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 118.87 93.23 25.64 9.00e-01 1.23e+00 8.11e+02 angle pdb=" N GLU A 39 " pdb=" CA GLU A 39 " pdb=" C GLU A 39 " ideal model delta sigma weight residual 111.00 50.01 60.99 2.80e+00 1.28e-01 4.74e+02 angle pdb=" CA PHE D 83 " pdb=" C PHE D 83 " pdb=" N LEU D 84 " ideal model delta sigma weight residual 118.38 90.25 28.13 1.30e+00 5.92e-01 4.68e+02 angle pdb=" CA LEU B 240 " pdb=" C LEU B 240 " pdb=" N VAL B 241 " ideal model delta sigma weight residual 117.39 92.00 25.39 1.24e+00 6.50e-01 4.19e+02 angle pdb=" CA GLN A 366 " pdb=" C GLN A 366 " pdb=" N VAL A 367 " ideal model delta sigma weight residual 116.01 85.37 30.64 1.51e+00 4.39e-01 4.12e+02 ... (remaining 5433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.18: 1708 14.18 - 28.35: 52 28.35 - 42.53: 11 42.53 - 56.70: 6 56.70 - 70.88: 2 Dihedral angle restraints: 1779 sinusoidal: 6 harmonic: 1773 Sorted by residual: dihedral pdb=" CA LYS A 38 " pdb=" C LYS A 38 " pdb=" N GLU A 39 " pdb=" CA GLU A 39 " ideal model delta harmonic sigma weight residual -180.00 -109.12 -70.88 0 5.00e+00 4.00e-02 2.01e+02 dihedral pdb=" CA PHE D 63 " pdb=" C PHE D 63 " pdb=" N TYR D 64 " pdb=" CA TYR D 64 " ideal model delta harmonic sigma weight residual -180.00 -133.67 -46.33 0 5.00e+00 4.00e-02 8.59e+01 dihedral pdb=" CA ASP A 57 " pdb=" C ASP A 57 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta harmonic sigma weight residual 180.00 -134.14 -45.86 0 5.00e+00 4.00e-02 8.41e+01 ... (remaining 1776 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.041: 3 0.041 - 0.074: 1 0.074 - 0.107: 2 0.107 - 0.140: 1 0.140 - 0.173: 1 Chirality restraints: 8 Sorted by residual: chirality pdb=" C1' ATP A 501 " pdb=" C2' ATP A 501 " pdb=" N9 ATP A 501 " pdb=" O4' ATP A 501 " both_signs ideal model delta sigma weight residual False 2.41 2.24 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" C2' ATP B 401 " pdb=" C1' ATP B 401 " pdb=" C3' ATP B 401 " pdb=" O2' ATP B 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" C1' ATP B 401 " pdb=" C2' ATP B 401 " pdb=" N9 ATP B 401 " pdb=" O4' ATP B 401 " both_signs ideal model delta sigma weight residual False 2.41 2.50 -0.09 2.00e-01 2.50e+01 2.03e-01 ... (remaining 5 not shown) Planarity restraints: 2 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP A 501 " 0.023 2.00e-02 2.50e+03 1.59e-02 6.92e+00 pdb=" C2 ATP A 501 " 0.001 2.00e-02 2.50e+03 pdb=" C4 ATP A 501 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ATP A 501 " 0.000 2.00e-02 2.50e+03 pdb=" C6 ATP A 501 " 0.002 2.00e-02 2.50e+03 pdb=" C8 ATP A 501 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ATP A 501 " 0.000 2.00e-02 2.50e+03 pdb=" N3 ATP A 501 " 0.001 2.00e-02 2.50e+03 pdb=" N6 ATP A 501 " 0.003 2.00e-02 2.50e+03 pdb=" N7 ATP A 501 " -0.001 2.00e-02 2.50e+03 pdb=" N9 ATP A 501 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP B 401 " 0.001 2.00e-02 2.50e+03 7.78e-04 1.66e-02 pdb=" C2 ATP B 401 " -0.000 2.00e-02 2.50e+03 pdb=" C4 ATP B 401 " 0.002 2.00e-02 2.50e+03 pdb=" C5 ATP B 401 " 0.001 2.00e-02 2.50e+03 pdb=" C6 ATP B 401 " -0.000 2.00e-02 2.50e+03 pdb=" C8 ATP B 401 " -0.000 2.00e-02 2.50e+03 pdb=" N1 ATP B 401 " -0.000 2.00e-02 2.50e+03 pdb=" N3 ATP B 401 " -0.001 2.00e-02 2.50e+03 pdb=" N6 ATP B 401 " 0.000 2.00e-02 2.50e+03 pdb=" N7 ATP B 401 " -0.000 2.00e-02 2.50e+03 pdb=" N9 ATP B 401 " -0.002 2.00e-02 2.50e+03 Histogram of nonbonded interaction distances: 2.03 - 2.61: 44 2.61 - 3.18: 2284 3.18 - 3.75: 2819 3.75 - 4.33: 5699 4.33 - 4.90: 10226 Nonbonded interactions: 21072 Sorted by model distance: nonbonded pdb=" N LEU B 240 " pdb=" N VAL B 241 " model vdw 2.034 2.560 nonbonded pdb=" N PHE D 83 " pdb=" N LEU D 84 " model vdw 2.040 2.560 nonbonded pdb=" N LEU A 58 " pdb=" N ASP A 59 " model vdw 2.065 2.560 nonbonded pdb=" N SER C 196 " pdb=" N GLU C 197 " model vdw 2.166 2.560 nonbonded pdb=" C LYS A 38 " pdb=" C GLU A 39 " model vdw 2.190 2.800 ... (remaining 21067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.150 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3187 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 : 0.021 0.398 5415 Z= 1.606 Angle : 3.501 60.991 5438 Z= 2.353 Chirality : 0.091 0.173 8 Planarity : 0.011 0.016 2 Dihedral : 6.696 70.879 1779 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.49 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 1758 helix: -0.92 (0.18), residues: 641 sheet: -0.01 (0.26), residues: 340 loop : -1.34 (0.21), residues: 777 Details of bonding type rmsd/Z covalent geometry : bond 0.02083 / 1.61 ( 5415) covalent geometry : angle 3.50144 / 2.35 ( 5438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.248 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0207 time to fit residues: 2.0348 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.082228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.061193 restraints weight = 37687.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060625 restraints weight = 43826.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060059 restraints weight = 48967.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060059 restraints weight = 54765.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060059 restraints weight = 54765.481| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5415 Z= 0.208 Angle : 0.789 7.955 5438 Z= 0.480 Chirality : 0.087 0.150 8 Planarity : 0.003 0.005 2 Dihedral : 6.131 55.815 1779 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.15 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 1758 helix: 0.11 (0.20), residues: 564 sheet: 0.08 (0.29), residues: 274 loop : -0.62 (0.20), residues: 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.21 ( 5415) covalent geometry : angle 0.78907 / 0.48 ( 5438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.216 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0219 time to fit residues: 2.1274 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 63 optimal weight: 30.0000 chunk 26 optimal weight: 0.0050 chunk 143 optimal weight: 20.0000 chunk 174 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 157 optimal weight: 50.0000 chunk 126 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 85 optimal weight: 50.0000 chunk 23 optimal weight: 40.0000 overall best weight: 6.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.064011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.047264 restraints weight = 41662.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046907 restraints weight = 45675.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046907 restraints weight = 49720.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046907 restraints weight = 49720.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046907 restraints weight = 49720.717| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 1.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5415 Z= 0.215 Angle : 0.859 11.875 5438 Z= 0.530 Chirality : 0.044 0.086 8 Planarity : 0.011 0.013 2 Dihedral : 7.393 76.214 1779 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.22 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.19), residues: 1758 helix: -0.90 (0.21), residues: 492 sheet: -0.11 (0.33), residues: 224 loop : -0.81 (0.19), residues: 1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.22 ( 5415) covalent geometry : angle 0.85890 / 0.53 ( 5438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.257 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0223 time to fit residues: 2.1217 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 76 optimal weight: 0.2980 chunk 9 optimal weight: 9.9990 chunk 82 optimal weight: 0.0000 chunk 173 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 63 optimal weight: 40.0000 chunk 93 optimal weight: 50.0000 chunk 51 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 overall best weight: 5.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044155 restraints weight = 43089.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044155 restraints weight = 46578.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044155 restraints weight = 46578.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044155 restraints weight = 46578.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044155 restraints weight = 46578.174| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 1.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 5415 Z= 0.161 Angle : 0.592 4.765 5438 Z= 0.384 Chirality : 0.030 0.063 8 Planarity : 0.001 0.001 2 Dihedral : 5.830 73.201 1779 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.97 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.19), residues: 1758 helix: -1.12 (0.22), residues: 478 sheet: -0.51 (0.32), residues: 224 loop : -0.81 (0.19), residues: 1056 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.16 ( 5415) covalent geometry : angle 0.59205 / 0.38 ( 5438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.260 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0217 time to fit residues: 2.0916 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 128 optimal weight: 30.0000 chunk 34 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 131 optimal weight: 7.9990 chunk 23 optimal weight: 40.0000 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 40.0000 overall best weight: 13.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047839 restraints weight = 34035.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.047316 restraints weight = 42164.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.047315 restraints weight = 50541.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.047315 restraints weight = 50555.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.047315 restraints weight = 50555.142| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 2.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 5415 Z= 0.341 Angle : 1.029 14.715 5438 Z= 0.659 Chirality : 0.042 0.089 8 Planarity : 0.004 0.006 2 Dihedral : 8.923 71.868 1779 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 28.26 Ramachandran Plot: Outliers : 0.80 % Allowed : 13.71 % Favored : 85.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.19), residues: 1758 helix: -3.03 (0.20), residues: 402 sheet: -1.22 (0.37), residues: 166 loop : -1.75 (0.18), residues: 1190 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.34 ( 5415) covalent geometry : angle 1.02864 / 0.66 ( 5438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.254 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0202 time to fit residues: 1.8959 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 50.0000 chunk 74 optimal weight: 0.0170 chunk 136 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 chunk 46 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 173 optimal weight: 0.0470 chunk 135 optimal weight: 0.0040 chunk 88 optimal weight: 30.0000 chunk 126 optimal weight: 50.0000 overall best weight: 5.6134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.052896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.039118 restraints weight = 46363.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.039117 restraints weight = 48457.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.039117 restraints weight = 48457.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.039117 restraints weight = 48457.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.039117 restraints weight = 48457.695| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 2.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5415 Z= 0.141 Angle : 0.544 6.421 5438 Z= 0.348 Chirality : 0.027 0.067 8 Planarity : 0.002 0.002 2 Dihedral : 5.843 79.176 1779 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.24 % Favored : 89.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.19), residues: 1758 helix: -2.56 (0.21), residues: 422 sheet: -1.38 (0.39), residues: 158 loop : -1.55 (0.19), residues: 1178 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.14 ( 5415) covalent geometry : angle 0.54371 / 0.35 ( 5438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.272 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0216 time to fit residues: 2.0199 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 87 optimal weight: 0.4980 chunk 56 optimal weight: 0.0270 chunk 5 optimal weight: 30.0000 chunk 105 optimal weight: 40.0000 chunk 174 optimal weight: 30.0000 chunk 83 optimal weight: 40.0000 chunk 43 optimal weight: 40.0000 chunk 163 optimal weight: 3.9990 overall best weight: 5.3046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.051685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.038202 restraints weight = 47353.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.038154 restraints weight = 49588.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.038154 restraints weight = 50605.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.038154 restraints weight = 50605.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.038154 restraints weight = 50605.583| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 2.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5415 Z= 0.146 Angle : 0.552 7.145 5438 Z= 0.351 Chirality : 0.020 0.035 8 Planarity : 0.002 0.002 2 Dihedral : 5.715 73.819 1779 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.51 % Favored : 85.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.19), residues: 1758 helix: -2.27 (0.22), residues: 426 sheet: -1.45 (0.44), residues: 136 loop : -1.63 (0.18), residues: 1196 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.15 ( 5415) covalent geometry : angle 0.55169 / 0.35 ( 5438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.321 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0218 time to fit residues: 2.1846 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 50.0000 chunk 143 optimal weight: 30.0000 chunk 46 optimal weight: 0.1980 chunk 167 optimal weight: 40.0000 chunk 148 optimal weight: 7.9990 chunk 61 optimal weight: 40.0000 chunk 141 optimal weight: 50.0000 chunk 50 optimal weight: 0.0010 chunk 132 optimal weight: 0.0170 overall best weight: 3.0428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.038634 restraints weight = 46203.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.038606 restraints weight = 48516.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.038606 restraints weight = 49048.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.038606 restraints weight = 49048.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.038606 restraints weight = 49048.440| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 2.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 5415 Z= 0.083 Angle : 0.389 6.485 5438 Z= 0.243 Chirality : 0.013 0.027 8 Planarity : 0.001 0.001 2 Dihedral : 4.553 73.357 1779 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.39 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.20), residues: 1758 helix: -1.76 (0.23), residues: 446 sheet: -1.45 (0.43), residues: 142 loop : -1.44 (0.19), residues: 1170 Details of bonding type rmsd/Z covalent geometry : bond 0.00114 / 0.08 ( 5415) covalent geometry : angle 0.38904 / 0.24 ( 5438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.274 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0238 time to fit residues: 2.2084 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 20 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 55 optimal weight: 40.0000 chunk 146 optimal weight: 30.0000 chunk 166 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 118 optimal weight: 0.0000 chunk 106 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 0.3980 chunk 78 optimal weight: 40.0000 overall best weight: 7.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.050107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.036985 restraints weight = 48481.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.036985 restraints weight = 50689.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.036985 restraints weight = 50694.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.036985 restraints weight = 50694.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.036985 restraints weight = 50694.706| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 2.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5415 Z= 0.190 Angle : 0.627 7.661 5438 Z= 0.407 Chirality : 0.021 0.045 8 Planarity : 0.002 0.002 2 Dihedral : 6.174 70.973 1779 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 15.76 % Favored : 83.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.19), residues: 1758 helix: -2.23 (0.22), residues: 444 sheet: -1.62 (0.44), residues: 137 loop : -1.89 (0.18), residues: 1177 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.19 ( 5415) covalent geometry : angle 0.62708 / 0.41 ( 5438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.259 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0216 time to fit residues: 2.0725 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 54 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 26 optimal weight: 40.0000 chunk 59 optimal weight: 30.0000 chunk 126 optimal weight: 50.0000 chunk 2 optimal weight: 20.0000 chunk 36 optimal weight: 0.0980 chunk 47 optimal weight: 20.0000 chunk 109 optimal weight: 40.0000 chunk 157 optimal weight: 20.0000 overall best weight: 14.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.047300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.035315 restraints weight = 50468.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.035315 restraints weight = 52449.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.035315 restraints weight = 52455.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.035315 restraints weight = 52455.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.035315 restraints weight = 52455.550| |-----------------------------------------------------------------------------| r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 2.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5415 Z= 0.320 Angle : 0.984 20.658 5438 Z= 0.620 Chirality : 0.026 0.051 8 Planarity : 0.004 0.004 2 Dihedral : 8.271 80.531 1779 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 34.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 19.17 % Favored : 80.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 1.25 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.18), residues: 1758 helix: -3.33 (0.20), residues: 399 sheet: -2.08 (0.49), residues: 104 loop : -2.61 (0.17), residues: 1255 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.32 ( 5415) covalent geometry : angle 0.98449 / 0.62 ( 5438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.281 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0213 time to fit residues: 2.0689 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 85 optimal weight: 50.0000 chunk 6 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 80 optimal weight: 40.0000 chunk 148 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 142 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 118 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 overall best weight: 7.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.047502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.035422 restraints weight = 49526.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.035344 restraints weight = 50887.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.035222 restraints weight = 52571.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.035222 restraints weight = 54113.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.035222 restraints weight = 54115.972| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 2.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5415 Z= 0.187 Angle : 0.663 16.599 5438 Z= 0.411 Chirality : 0.024 0.037 8 Planarity : 0.002 0.002 2 Dihedral : 6.344 79.513 1779 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 17.18 % Favored : 82.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.19), residues: 1758 helix: -3.05 (0.21), residues: 404 sheet: -1.97 (0.48), residues: 112 loop : -2.51 (0.17), residues: 1242 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.19 ( 5415) covalent geometry : angle 0.66344 / 0.41 ( 5438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1012.44 seconds wall clock time: 18 minutes 27.43 seconds (1107.43 seconds total)