Starting phenix.real_space_refine on Thu Mar 6 07:50:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yw7_10960/03_2025/6yw7_10960.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yw7_10960/03_2025/6yw7_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_10960/03_2025/6yw7_10960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yw7_10960/03_2025/6yw7_10960.map" model { file = "/net/cci-nas-00/data/ceres_data/6yw7_10960/03_2025/6yw7_10960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yw7_10960/03_2025/6yw7_10960.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 14, 'HIS:plan': 9, 'TYR:plan': 18, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 20, 'GLU:plan': 32, 'ARG:plan': 22} 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: {'GLN:plan1': 6, 'HIS:plan': 11, 'TYR:plan': 12, 'ASN:plan1': 16, 'ASP:plan': 20, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 16} 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: {'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 7} 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: {'GLN:plan1': 8, 'ARG:plan': 16, 'TYR:plan': 12, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 14, 'GLU:plan': 20, 'ASP:plan': 17} 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: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 8, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 19, 'ARG:plan': 12} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 6} 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: {'GLN:plan1': 12, 'ASP:plan': 19, 'TYR:plan': 6, 'ASN:plan1': 14, 'TRP:plan': 13, 'HIS:plan': 13, 'PHE:plan': 15, 'GLU:plan': 15, 'ARG:plan': 13} 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: 4.68, per 1000 atoms: 0.86 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: 1.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.00 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: 1.34 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 - 16.28: 1758 16.28 - 32.56: 58 32.56 - 48.84: 17 48.84 - 65.12: 4 65.12 - 81.40: 4 Dihedral angle restraints: 1841 sinusoidal: 68 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 1838 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: 1.190 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.680 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3204 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 : 8.081 81.400 1841 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (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 *********************** 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 : 0.725 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: 0.0464 time to fit residues: 4.7260 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 : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 0.1980 chunk 73 optimal weight: 40.0000 chunk 45 optimal weight: 0.1980 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 chunk 83 optimal weight: 0.0570 chunk 102 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 overall best weight: 1.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.099471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075571 restraints weight = 34325.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074697 restraints weight = 40196.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074249 restraints weight = 45621.614| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.031 5415 Z= 0.081 Angle : 0.435 6.661 5438 Z= 0.255 Chirality : 0.040 0.066 8 Planarity : 0.002 0.002 2 Dihedral : 5.060 65.888 1841 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.28 % Favored : 97.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1758 helix: 1.21 (0.21), residues: 639 sheet: 0.55 (0.28), residues: 319 loop : -0.49 (0.22), residues: 800 *********************** 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 : 0.782 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: 0.0453 time to fit residues: 4.7624 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 : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 42 optimal weight: 20.0000 chunk 43 optimal weight: 40.0000 chunk 103 optimal weight: 0.9990 chunk 118 optimal weight: 50.0000 chunk 49 optimal weight: 0.9990 chunk 67 optimal weight: 50.0000 chunk 169 optimal weight: 30.0000 chunk 60 optimal weight: 0.0070 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.074266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055325 restraints weight = 39194.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054945 restraints weight = 44291.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.054557 restraints weight = 48032.942| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 1.0253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5415 Z= 0.128 Angle : 0.608 6.579 5438 Z= 0.368 Chirality : 0.030 0.053 8 Planarity : 0.001 0.001 2 Dihedral : 6.030 83.595 1841 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.44 % Favored : 95.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1758 helix: 1.38 (0.21), residues: 555 sheet: -0.04 (0.30), residues: 277 loop : -0.13 (0.21), residues: 926 *********************** 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 : 0.869 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: 0.0448 time to fit residues: 4.7222 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 : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 126 optimal weight: 50.0000 chunk 79 optimal weight: 0.0670 chunk 34 optimal weight: 40.0000 chunk 80 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 150 optimal weight: 50.0000 chunk 87 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 chunk 145 optimal weight: 40.0000 chunk 27 optimal weight: 0.0980 chunk 88 optimal weight: 10.0000 overall best weight: 8.0328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.060867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.044552 restraints weight = 43521.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.044552 restraints weight = 46982.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.044552 restraints weight = 46982.090| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 1.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5415 Z= 0.256 Angle : 0.831 13.665 5438 Z= 0.535 Chirality : 0.061 0.138 8 Planarity : 0.008 0.010 2 Dihedral : 8.380 89.259 1841 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.09 % Favored : 93.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 1758 helix: -1.60 (0.20), residues: 477 sheet: -0.09 (0.33), residues: 242 loop : -0.80 (0.19), residues: 1039 *********************** 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 : 0.722 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: 0.0441 time to fit residues: 4.8277 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 : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 23 optimal weight: 0.8980 chunk 126 optimal weight: 40.0000 chunk 40 optimal weight: 20.0000 chunk 145 optimal weight: 40.0000 chunk 158 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 44 optimal weight: 20.0000 chunk 101 optimal weight: 0.0570 chunk 17 optimal weight: 40.0000 chunk 72 optimal weight: 50.0000 overall best weight: 5.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.058769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.043412 restraints weight = 43606.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.043412 restraints weight = 46645.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.043412 restraints weight = 46645.687| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 1.7449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5415 Z= 0.139 Angle : 0.506 3.952 5438 Z= 0.331 Chirality : 0.019 0.032 8 Planarity : 0.002 0.003 2 Dihedral : 6.008 77.870 1841 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.86 % Favored : 93.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.20), residues: 1758 helix: -0.99 (0.22), residues: 493 sheet: -0.32 (0.32), residues: 249 loop : -0.66 (0.20), residues: 1016 *********************** 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 : 0.979 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: 0.0438 time to fit residues: 4.6019 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 : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 142 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 172 optimal weight: 50.0000 chunk 121 optimal weight: 0.0470 chunk 42 optimal weight: 50.0000 chunk 152 optimal weight: 40.0000 chunk 90 optimal weight: 20.0000 chunk 111 optimal weight: 0.0010 chunk 153 optimal weight: 20.0000 chunk 162 optimal weight: 30.0000 chunk 41 optimal weight: 3.9990 overall best weight: 8.8094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.050819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.038834 restraints weight = 67705.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.038576 restraints weight = 77726.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.038413 restraints weight = 87466.937| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 2.0470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5415 Z= 0.241 Angle : 0.786 11.133 5438 Z= 0.506 Chirality : 0.029 0.053 8 Planarity : 0.003 0.004 2 Dihedral : 8.236 79.739 1841 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.30 % Favored : 89.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.19), residues: 1758 helix: -2.25 (0.21), residues: 428 sheet: -1.07 (0.38), residues: 168 loop : -1.40 (0.18), residues: 1162 *********************** 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 : 0.726 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: 0.0443 time to fit residues: 4.5721 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 : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 102 optimal weight: 10.0000 chunk 35 optimal weight: 0.0000 chunk 32 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 128 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 163 optimal weight: 6.9990 chunk 76 optimal weight: 0.0020 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.040601 restraints weight = 45304.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.040429 restraints weight = 47916.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 12)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.040429 restraints weight = 50271.248| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 2.0066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 5415 Z= 0.066 Angle : 0.380 4.491 5438 Z= 0.235 Chirality : 0.016 0.027 8 Planarity : 0.001 0.001 2 Dihedral : 5.414 79.614 1841 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.57 % Favored : 94.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.20), residues: 1758 helix: -1.15 (0.22), residues: 487 sheet: -0.93 (0.34), residues: 220 loop : -1.17 (0.20), residues: 1051 *********************** 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 : 0.775 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: 0.0449 time to fit residues: 4.7222 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 : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 149 optimal weight: 30.0000 chunk 97 optimal weight: 50.0000 chunk 14 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 29 optimal weight: 0.0040 chunk 141 optimal weight: 50.0000 chunk 32 optimal weight: 0.0980 chunk 36 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 169 optimal weight: 0.0070 chunk 34 optimal weight: 0.9990 overall best weight: 2.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.040481 restraints weight = 45488.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.040451 restraints weight = 48209.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.040451 restraints weight = 48766.006| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 2.0251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 5415 Z= 0.071 Angle : 0.333 3.420 5438 Z= 0.213 Chirality : 0.021 0.044 8 Planarity : 0.001 0.001 2 Dihedral : 5.068 79.502 1841 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.08 % Favored : 91.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1758 helix: -0.55 (0.24), residues: 473 sheet: -1.01 (0.34), residues: 220 loop : -1.00 (0.20), residues: 1065 *********************** 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 : 0.765 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: 0.0461 time to fit residues: 4.8560 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 : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 57 optimal weight: 4.9990 chunk 87 optimal weight: 0.0870 chunk 158 optimal weight: 30.0000 chunk 54 optimal weight: 30.0000 chunk 172 optimal weight: 0.0040 chunk 70 optimal weight: 0.0010 chunk 81 optimal weight: 50.0000 chunk 9 optimal weight: 9.9990 chunk 38 optimal weight: 0.0070 chunk 30 optimal weight: 0.0060 chunk 66 optimal weight: 0.0770 overall best weight: 0.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.042006 restraints weight = 42639.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.042004 restraints weight = 45604.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.042004 restraints weight = 45636.408| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 1.9908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 5415 Z= 0.043 Angle : 0.247 5.337 5438 Z= 0.147 Chirality : 0.018 0.033 8 Planarity : 0.001 0.002 2 Dihedral : 4.397 80.006 1841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1758 helix: 0.55 (0.25), residues: 487 sheet: -0.71 (0.35), residues: 234 loop : -0.82 (0.20), residues: 1037 *********************** 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 : 0.783 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: 0.0448 time to fit residues: 4.6887 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 : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 15 optimal weight: 20.0000 chunk 41 optimal weight: 0.0030 chunk 167 optimal weight: 40.0000 chunk 174 optimal weight: 40.0000 chunk 27 optimal weight: 0.0470 chunk 149 optimal weight: 40.0000 chunk 135 optimal weight: 30.0000 chunk 156 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 139 optimal weight: 40.0000 overall best weight: 9.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.036584 restraints weight = 64177.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.036292 restraints weight = 75788.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.036056 restraints weight = 86776.634| |-----------------------------------------------------------------------------| r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 2.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5415 Z= 0.237 Angle : 0.680 6.273 5438 Z= 0.455 Chirality : 0.026 0.059 8 Planarity : 0.003 0.004 2 Dihedral : 7.039 85.294 1841 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.92 % Favored : 88.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.20), residues: 1758 helix: -1.32 (0.23), residues: 427 sheet: -0.72 (0.38), residues: 190 loop : -1.17 (0.19), residues: 1141 ********************** 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 : 0.652 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: 0.0467 time to fit residues: 4.9156 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 : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 77 optimal weight: 40.0000 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 50.0000 chunk 117 optimal weight: 50.0000 chunk 131 optimal weight: 30.0000 chunk 27 optimal weight: 0.0870 chunk 130 optimal weight: 30.0000 chunk 112 optimal weight: 20.0000 overall best weight: 9.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.036963 restraints weight = 48812.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.036963 restraints weight = 50688.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.036963 restraints weight = 50688.745| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 2.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5415 Z= 0.232 Angle : 0.707 9.881 5438 Z= 0.457 Chirality : 0.027 0.058 8 Planarity : 0.002 0.002 2 Dihedral : 7.504 87.744 1841 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.26 % Favored : 88.51 % 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 : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.19), residues: 1758 helix: -2.14 (0.22), residues: 428 sheet: -1.43 (0.39), residues: 167 loop : -1.70 (0.18), residues: 1163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.25 seconds wall clock time: 32 minutes 10.40 seconds (1930.40 seconds total)