Starting phenix.real_space_refine on Tue Mar 3 13:40:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yw7_10960/03_2026/6yw7_10960.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yw7_10960/03_2026/6yw7_10960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6yw7_10960/03_2026/6yw7_10960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yw7_10960/03_2026/6yw7_10960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yw7_10960/03_2026/6yw7_10960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yw7_10960/03_2026/6yw7_10960.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 6 5.49 5 C 3596 2.51 5 N 1798 2.21 5 O 26 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5426 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 1188 Classifications: {'peptide': 396} Incomplete info: {'n_c_alpha_c_only': 396} Link IDs: {'PTRANS': 26, 'TRANS': 369} Chain breaks: 2 Unresolved chain link angles: 421 Unresolved non-hydrogen bonds: 2072 Unresolved non-hydrogen angles: 2818 Unresolved non-hydrogen dihedrals: 1103 Unresolved non-hydrogen chiralities: 481 Planarities with less than four sites: {'ARG:plan': 22, 'ASP:plan': 24, 'TYR:plan': 18, 'ASN:plan1': 10, 'GLU:plan': 32, 'GLN:plan1': 14, 'PHE:plan': 20, 'TRP:plan': 5, 'HIS:plan': 9} Unresolved non-hydrogen planarities: 818 Chain: "D" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 852 Classifications: {'peptide': 284} Incomplete info: {'n_c_alpha_c_only': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved chain link angles: 292 Unresolved non-hydrogen bonds: 1489 Unresolved non-hydrogen angles: 2017 Unresolved non-hydrogen dihedrals: 780 Unresolved non-hydrogen chiralities: 346 Planarities with less than four sites: {'GLU:plan': 21, 'ASN:plan1': 16, 'ARG:plan': 16, 'PHE:plan': 18, 'ASP:plan': 20, 'TYR:plan': 12, 'HIS:plan': 11, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 620 Chain: "E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 510 Classifications: {'peptide': 170} Incomplete info: {'n_c_alpha_c_only': 170} Link IDs: {'PTRANS': 11, 'TRANS': 158} Chain breaks: 1 Unresolved chain link angles: 180 Unresolved non-hydrogen bonds: 903 Unresolved non-hydrogen angles: 1215 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 202 Planarities with less than four sites: {'ASP:plan': 9, 'ASN:plan1': 10, 'ARG:plan': 7, 'GLN:plan1': 9, 'PHE:plan': 9, 'GLU:plan': 12, 'TYR:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 342 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 858 Classifications: {'peptide': 286} Incomplete info: {'n_c_alpha_c_only': 286} Link IDs: {'PTRANS': 14, 'TRANS': 271} Chain breaks: 3 Unresolved chain link angles: 299 Unresolved non-hydrogen bonds: 1467 Unresolved non-hydrogen angles: 1992 Unresolved non-hydrogen dihedrals: 764 Unresolved non-hydrogen chiralities: 353 Planarities with less than four sites: {'ASP:plan': 17, 'ASN:plan1': 7, 'PHE:plan': 14, 'TYR:plan': 12, 'GLU:plan': 20, 'HIS:plan': 8, 'TRP:plan': 2, 'GLN:plan1': 8, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 550 Chain: "F" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 495 Classifications: {'peptide': 165} Incomplete info: {'n_c_alpha_c_only': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Unresolved chain link angles: 168 Unresolved non-hydrogen bonds: 886 Unresolved non-hydrogen angles: 1190 Unresolved non-hydrogen dihedrals: 462 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'ARG:plan': 12, 'TYR:plan': 3, 'GLN:plan1': 5, 'GLU:plan': 19, 'ASN:plan1': 8, 'PHE:plan': 11, 'HIS:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 335 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 417 Classifications: {'peptide': 139} Incomplete info: {'n_c_alpha_c_only': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 1 Unresolved chain link angles: 142 Unresolved non-hydrogen bonds: 658 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 164 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 4, 'ASP:plan': 12, 'GLU:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 7, 'GLN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 230 Chain: "C" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 1044 Classifications: {'peptide': 348} Incomplete info: {'n_c_alpha_c_only': 348} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain breaks: 1 Unresolved chain link angles: 360 Unresolved non-hydrogen bonds: 1764 Unresolved non-hydrogen angles: 2409 Unresolved non-hydrogen dihedrals: 949 Unresolved non-hydrogen chiralities: 420 Planarities with less than four sites: {'HIS:plan': 13, 'GLN:plan1': 12, 'PHE:plan': 15, 'GLU:plan': 15, 'TRP:plan': 13, 'ASN:plan1': 14, 'ARG:plan': 13, 'ASP:plan': 19, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 666 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.91, per 1000 atoms: 0.35 Number of scatterers: 5426 At special positions: 0 Unit cell: (138.43, 91.56, 136.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 6 15.00 O 26 8.00 N 1798 7.00 C 3596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 645.3 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.54 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.710 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 1758 helix: -0.92 (0.18), residues: 641 sheet: -0.01 (0.26), residues: 340 loop : -1.34 (0.21), residues: 777 Details of bonding type rmsd covalent geometry : bond 0.02083 ( 5415) covalent geometry : angle 3.50144 ( 5438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.234 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0207 time to fit residues: 1.9126 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 : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.082325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061594 restraints weight = 37621.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060784 restraints weight = 42897.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060297 restraints weight = 48445.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059749 restraints weight = 53366.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059749 restraints weight = 57752.929| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.7288 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= 0.212 Angle : 0.778 7.870 5438 Z= 0.474 Chirality : 0.069 0.170 8 Planarity : 0.002 0.003 2 Dihedral : 6.990 69.673 1841 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.10 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.19), residues: 1758 helix: 0.08 (0.20), residues: 568 sheet: 0.17 (0.29), residues: 269 loop : -0.66 (0.20), residues: 921 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5415) covalent geometry : angle 0.77786 ( 5438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.232 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0207 time to fit residues: 2.0261 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 : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 63 optimal weight: 30.0000 chunk 26 optimal weight: 0.4980 chunk 143 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 157 optimal weight: 50.0000 chunk 126 optimal weight: 0.0050 chunk 73 optimal weight: 0.0050 chunk 85 optimal weight: 50.0000 chunk 23 optimal weight: 30.0000 overall best weight: 2.9012 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.071499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053089 restraints weight = 39816.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.052759 restraints weight = 44908.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052232 restraints weight = 49228.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052232 restraints weight = 53505.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052232 restraints weight = 53505.935| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 1.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5415 Z= 0.131 Angle : 0.604 7.255 5438 Z= 0.364 Chirality : 0.048 0.098 8 Planarity : 0.001 0.001 2 Dihedral : 5.844 73.626 1841 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1758 helix: 1.08 (0.21), residues: 575 sheet: 0.17 (0.31), residues: 255 loop : -0.31 (0.21), residues: 928 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 5415) covalent geometry : angle 0.60362 ( 5438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.222 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: 0.0188 time to fit residues: 1.7869 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 : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 76 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 173 optimal weight: 50.0000 chunk 3 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 50.0000 chunk 93 optimal weight: 50.0000 chunk 51 optimal weight: 40.0000 chunk 19 optimal weight: 9.9990 chunk 52 optimal weight: 0.0000 overall best weight: 4.7590 ------------------------------------------------------------------------------- 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 = 0.3191 r_free = 0.3191 target = 0.061585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.053326 restraints weight = 82680.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052945 restraints weight = 103577.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.052530 restraints weight = 124043.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.052524 restraints weight = 145034.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.052514 restraints weight = 145587.358| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 1.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 5415 Z= 0.167 Angle : 0.637 8.014 5438 Z= 0.408 Chirality : 0.054 0.104 8 Planarity : 0.004 0.005 2 Dihedral : 7.110 80.847 1841 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.29 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 1758 helix: -0.10 (0.22), residues: 502 sheet: -0.15 (0.32), residues: 252 loop : -0.41 (0.20), residues: 1004 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5415) covalent geometry : angle 0.63722 ( 5438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.154 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: 0.0163 time to fit residues: 1.4967 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 : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 128 optimal weight: 30.0000 chunk 34 optimal weight: 40.0000 chunk 73 optimal weight: 0.1980 chunk 172 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 105 optimal weight: 30.0000 chunk 26 optimal weight: 50.0000 chunk 131 optimal weight: 0.0170 chunk 23 optimal weight: 30.0000 chunk 147 optimal weight: 30.0000 chunk 44 optimal weight: 50.0000 overall best weight: 16.0430 ------------------------------------------------------------------------------- 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 = 0.3088 r_free = 0.3088 target = 0.052182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.038632 restraints weight = 49465.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.038632 restraints weight = 50760.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.038632 restraints weight = 50761.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.038632 restraints weight = 50761.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.038632 restraints weight = 50761.821| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 2.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 5415 Z= 0.391 Angle : 1.201 22.954 5438 Z= 0.757 Chirality : 0.047 0.100 8 Planarity : 0.005 0.005 2 Dihedral : 10.766 84.204 1841 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 32.47 Ramachandran Plot: Outliers : 0.51 % Allowed : 13.37 % Favored : 86.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 1.25 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.18), residues: 1758 helix: -3.29 (0.19), residues: 387 sheet: -1.27 (0.38), residues: 144 loop : -1.82 (0.18), residues: 1227 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 5415) covalent geometry : angle 1.20124 ( 5438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.245 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: 0.0209 time to fit residues: 1.9645 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 : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 40.0000 chunk 74 optimal weight: 0.0370 chunk 136 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 70 optimal weight: 30.0000 chunk 46 optimal weight: 0.0670 chunk 80 optimal weight: 8.9990 chunk 173 optimal weight: 50.0000 chunk 135 optimal weight: 0.2980 chunk 88 optimal weight: 4.9990 chunk 126 optimal weight: 40.0000 overall best weight: 2.8800 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.053548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.039548 restraints weight = 46415.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.039548 restraints weight = 49066.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.039548 restraints weight = 49066.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.039548 restraints weight = 49066.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.039548 restraints weight = 49066.676| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 2.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 5415 Z= 0.095 Angle : 0.489 5.519 5438 Z= 0.312 Chirality : 0.022 0.036 8 Planarity : 0.001 0.001 2 Dihedral : 6.538 87.502 1841 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.91 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.19), residues: 1758 helix: -2.30 (0.22), residues: 425 sheet: -1.12 (0.39), residues: 158 loop : -1.60 (0.18), residues: 1175 Details of bonding type rmsd covalent geometry : bond 0.00131 ( 5415) covalent geometry : angle 0.48885 ( 5438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.218 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: 0.0181 time to fit residues: 1.7643 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 : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 108 optimal weight: 30.0000 chunk 99 optimal weight: 0.0470 chunk 97 optimal weight: 50.0000 chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 174 optimal weight: 50.0000 chunk 83 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 163 optimal weight: 6.9990 overall best weight: 5.0088 ------------------------------------------------------------------------------- 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 = 0.3091 r_free = 0.3091 target = 0.052366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.038753 restraints weight = 47671.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.038613 restraints weight = 50046.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.038613 restraints weight = 51705.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.038613 restraints weight = 51705.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.038613 restraints weight = 51705.125| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 2.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5415 Z= 0.138 Angle : 0.531 8.429 5438 Z= 0.337 Chirality : 0.027 0.058 8 Planarity : 0.003 0.003 2 Dihedral : 6.437 85.333 1841 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.08 % Favored : 86.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.19), residues: 1758 helix: -2.00 (0.23), residues: 414 sheet: -1.11 (0.40), residues: 160 loop : -1.62 (0.18), residues: 1184 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 5415) covalent geometry : angle 0.53064 ( 5438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.209 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0213 time to fit residues: 1.9726 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 20.0000 chunk 134 optimal weight: 0.0870 chunk 75 optimal weight: 50.0000 chunk 143 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 167 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 61 optimal weight: 50.0000 chunk 141 optimal weight: 50.0000 chunk 50 optimal weight: 20.0000 chunk 132 optimal weight: 0.0030 overall best weight: 6.0174 ------------------------------------------------------------------------------- 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 = 0.3065 r_free = 0.3065 target = 0.050991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.037741 restraints weight = 48081.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.037741 restraints weight = 50172.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.037741 restraints weight = 50173.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.037741 restraints weight = 50173.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.037741 restraints weight = 50173.157| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 2.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5415 Z= 0.159 Angle : 0.569 6.714 5438 Z= 0.366 Chirality : 0.018 0.033 8 Planarity : 0.001 0.001 2 Dihedral : 6.701 86.269 1841 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.17 % Favored : 87.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.19), residues: 1758 helix: -2.32 (0.22), residues: 418 sheet: -1.45 (0.45), residues: 125 loop : -1.66 (0.18), residues: 1215 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 5415) covalent geometry : angle 0.56895 ( 5438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.241 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: 0.0167 time to fit residues: 1.5977 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 : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 20 optimal weight: 0.0370 chunk 53 optimal weight: 8.9990 chunk 55 optimal weight: 40.0000 chunk 146 optimal weight: 40.0000 chunk 166 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 overall best weight: 8.0066 ------------------------------------------------------------------------------- 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 = 0.3017 r_free = 0.3017 target = 0.049252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.036367 restraints weight = 49086.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.036367 restraints weight = 51167.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.036367 restraints weight = 51167.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.036367 restraints weight = 51167.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.036367 restraints weight = 51167.616| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 2.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5415 Z= 0.201 Angle : 0.684 12.925 5438 Z= 0.433 Chirality : 0.028 0.062 8 Planarity : 0.003 0.003 2 Dihedral : 7.252 82.578 1841 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.70 % Favored : 83.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.19), residues: 1758 helix: -2.50 (0.22), residues: 423 sheet: -1.90 (0.43), residues: 131 loop : -1.98 (0.18), residues: 1204 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5415) covalent geometry : angle 0.68448 ( 5438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.240 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0216 time to fit residues: 2.0271 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 : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 54 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 128 optimal weight: 40.0000 chunk 26 optimal weight: 40.0000 chunk 59 optimal weight: 30.0000 chunk 126 optimal weight: 50.0000 chunk 2 optimal weight: 30.0000 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 109 optimal weight: 40.0000 chunk 157 optimal weight: 20.0000 overall best weight: 14.1996 ------------------------------------------------------------------------------- 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 = 0.2806 r_free = 0.2806 target = 0.044182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.032321 restraints weight = 67064.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.032056 restraints weight = 78712.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.031831 restraints weight = 89791.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.031831 restraints weight = 100518.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.031831 restraints weight = 100518.134| |-----------------------------------------------------------------------------| r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 2.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 5415 Z= 0.322 Angle : 0.992 20.951 5438 Z= 0.613 Chirality : 0.029 0.053 8 Planarity : 0.004 0.005 2 Dihedral : 9.226 80.212 1841 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 33.56 Ramachandran Plot: Outliers : 0.34 % Allowed : 19.57 % Favored : 80.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 1.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.18), residues: 1758 helix: -3.47 (0.19), residues: 412 sheet: -2.38 (0.46), residues: 111 loop : -2.62 (0.17), residues: 1235 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 5415) covalent geometry : angle 0.99164 ( 5438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.223 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: 0.0191 time to fit residues: 1.8071 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 : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 85 optimal weight: 40.0000 chunk 6 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 chunk 148 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 67 optimal weight: 50.0000 chunk 118 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- 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 = 0.2969 r_free = 0.2969 target = 0.046745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.035082 restraints weight = 50403.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.035012 restraints weight = 51937.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.035012 restraints weight = 53457.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.035012 restraints weight = 53457.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.035012 restraints weight = 53457.985| |-----------------------------------------------------------------------------| r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 2.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5415 Z= 0.249 Angle : 0.792 16.758 5438 Z= 0.494 Chirality : 0.026 0.056 8 Planarity : 0.003 0.003 2 Dihedral : 7.896 79.903 1841 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 20.08 % Favored : 79.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.18), residues: 1758 helix: -3.51 (0.19), residues: 408 sheet: -1.92 (0.47), residues: 108 loop : -2.76 (0.17), residues: 1242 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5415) covalent geometry : angle 0.79214 ( 5438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 932.63 seconds wall clock time: 16 minutes 29.07 seconds (989.07 seconds total)