Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 04:38:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2023/6yw7_10960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2023/6yw7_10960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2023/6yw7_10960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2023/6yw7_10960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2023/6yw7_10960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2023/6yw7_10960_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5426 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 1188 Classifications: {'peptide': 396} Incomplete info: {'n_c_alpha_c_only': 396} Link IDs: {'PTRANS': 26, 'TRANS': 369} Chain breaks: 2 Unresolved chain link angles: 421 Unresolved non-hydrogen bonds: 2072 Unresolved non-hydrogen angles: 2818 Unresolved non-hydrogen dihedrals: 1103 Unresolved non-hydrogen chiralities: 481 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 9, 'TYR:plan': 18, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 20, 'GLU:plan': 32, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 818 Chain: "D" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 852 Classifications: {'peptide': 284} Incomplete info: {'n_c_alpha_c_only': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved chain link angles: 292 Unresolved non-hydrogen bonds: 1489 Unresolved non-hydrogen angles: 2017 Unresolved non-hydrogen dihedrals: 780 Unresolved non-hydrogen chiralities: 346 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 11, 'TYR:plan': 12, 'ASN:plan1': 16, 'ASP:plan': 20, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 620 Chain: "E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 510 Classifications: {'peptide': 170} Incomplete info: {'n_c_alpha_c_only': 170} Link IDs: {'PTRANS': 11, 'TRANS': 158} Chain breaks: 1 Unresolved chain link angles: 180 Unresolved non-hydrogen bonds: 903 Unresolved non-hydrogen angles: 1215 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 202 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 342 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 858 Classifications: {'peptide': 286} Incomplete info: {'n_c_alpha_c_only': 286} Link IDs: {'PTRANS': 14, 'TRANS': 271} Chain breaks: 3 Unresolved chain link angles: 299 Unresolved non-hydrogen bonds: 1467 Unresolved non-hydrogen angles: 1992 Unresolved non-hydrogen dihedrals: 764 Unresolved non-hydrogen chiralities: 353 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 16, 'TYR:plan': 12, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 14, 'GLU:plan': 20, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 550 Chain: "F" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 495 Classifications: {'peptide': 165} Incomplete info: {'n_c_alpha_c_only': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Unresolved chain link angles: 168 Unresolved non-hydrogen bonds: 886 Unresolved non-hydrogen angles: 1190 Unresolved non-hydrogen dihedrals: 462 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 8, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 335 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 417 Classifications: {'peptide': 139} Incomplete info: {'n_c_alpha_c_only': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 1 Unresolved chain link angles: 142 Unresolved non-hydrogen bonds: 658 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 164 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 230 Chain: "C" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 1044 Classifications: {'peptide': 348} Incomplete info: {'n_c_alpha_c_only': 348} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain breaks: 1 Unresolved chain link angles: 360 Unresolved non-hydrogen bonds: 1764 Unresolved non-hydrogen angles: 2409 Unresolved non-hydrogen dihedrals: 949 Unresolved non-hydrogen chiralities: 420 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 19, 'TYR:plan': 6, 'ASN:plan1': 14, 'TRP:plan': 13, 'HIS:plan': 13, 'PHE:plan': 15, 'GLU:plan': 15, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 666 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.26, per 1000 atoms: 0.79 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.7 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.87 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: 50.01 - 69.36: 1 69.36 - 88.71: 3 88.71 - 108.05: 367 108.05 - 127.40: 4986 127.40 - 146.75: 81 Bond angle restraints: 5438 Sorted by residual: angle pdb=" CA GLN B 267 " pdb=" C GLN B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 118.87 93.23 25.64 9.00e-01 1.23e+00 8.11e+02 angle pdb=" N GLU A 39 " pdb=" CA GLU A 39 " pdb=" C GLU A 39 " ideal model delta sigma weight residual 111.00 50.01 60.99 2.80e+00 1.28e-01 4.74e+02 angle pdb=" CA PHE D 83 " pdb=" C PHE D 83 " pdb=" N LEU D 84 " ideal model delta sigma weight residual 118.38 90.25 28.13 1.30e+00 5.92e-01 4.68e+02 angle pdb=" CA LEU B 240 " pdb=" C LEU B 240 " pdb=" N VAL B 241 " ideal model delta sigma weight residual 117.39 92.00 25.39 1.24e+00 6.50e-01 4.19e+02 angle pdb=" CA GLN A 366 " pdb=" C GLN A 366 " pdb=" N VAL A 367 " ideal model delta sigma weight residual 116.01 85.37 30.64 1.51e+00 4.39e-01 4.12e+02 ... (remaining 5433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.18: 1708 14.18 - 28.35: 52 28.35 - 42.53: 11 42.53 - 56.70: 6 56.70 - 70.88: 2 Dihedral angle restraints: 1779 sinusoidal: 6 harmonic: 1773 Sorted by residual: dihedral pdb=" CA LYS A 38 " pdb=" C LYS A 38 " pdb=" N GLU A 39 " pdb=" CA GLU A 39 " ideal model delta harmonic sigma weight residual -180.00 -109.12 -70.88 0 5.00e+00 4.00e-02 2.01e+02 dihedral pdb=" CA PHE D 63 " pdb=" C PHE D 63 " pdb=" N TYR D 64 " pdb=" CA TYR D 64 " ideal model delta harmonic sigma weight residual -180.00 -133.67 -46.33 0 5.00e+00 4.00e-02 8.59e+01 dihedral pdb=" CA ASP A 57 " pdb=" C ASP A 57 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta harmonic sigma weight residual 180.00 -134.14 -45.86 0 5.00e+00 4.00e-02 8.41e+01 ... (remaining 1776 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.041: 3 0.041 - 0.074: 1 0.074 - 0.107: 2 0.107 - 0.140: 1 0.140 - 0.173: 1 Chirality restraints: 8 Sorted by residual: chirality pdb=" C1' ATP A 501 " pdb=" C2' ATP A 501 " pdb=" N9 ATP A 501 " pdb=" O4' ATP A 501 " both_signs ideal model delta sigma weight residual False 2.41 2.24 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" C2' ATP B 401 " pdb=" C1' ATP B 401 " pdb=" C3' ATP B 401 " pdb=" O2' ATP B 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" C1' ATP B 401 " pdb=" C2' ATP B 401 " pdb=" N9 ATP B 401 " pdb=" O4' ATP B 401 " both_signs ideal model delta sigma weight residual False 2.41 2.50 -0.09 2.00e-01 2.50e+01 2.03e-01 ... (remaining 5 not shown) Planarity restraints: 2 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP A 501 " 0.023 2.00e-02 2.50e+03 1.59e-02 6.92e+00 pdb=" C2 ATP A 501 " 0.001 2.00e-02 2.50e+03 pdb=" C4 ATP A 501 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ATP A 501 " 0.000 2.00e-02 2.50e+03 pdb=" C6 ATP A 501 " 0.002 2.00e-02 2.50e+03 pdb=" C8 ATP A 501 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ATP A 501 " 0.000 2.00e-02 2.50e+03 pdb=" N3 ATP A 501 " 0.001 2.00e-02 2.50e+03 pdb=" N6 ATP A 501 " 0.003 2.00e-02 2.50e+03 pdb=" N7 ATP A 501 " -0.001 2.00e-02 2.50e+03 pdb=" N9 ATP A 501 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP B 401 " 0.001 2.00e-02 2.50e+03 7.78e-04 1.66e-02 pdb=" C2 ATP B 401 " -0.000 2.00e-02 2.50e+03 pdb=" C4 ATP B 401 " 0.002 2.00e-02 2.50e+03 pdb=" C5 ATP B 401 " 0.001 2.00e-02 2.50e+03 pdb=" C6 ATP B 401 " -0.000 2.00e-02 2.50e+03 pdb=" C8 ATP B 401 " -0.000 2.00e-02 2.50e+03 pdb=" N1 ATP B 401 " -0.000 2.00e-02 2.50e+03 pdb=" N3 ATP B 401 " -0.001 2.00e-02 2.50e+03 pdb=" N6 ATP B 401 " 0.000 2.00e-02 2.50e+03 pdb=" N7 ATP B 401 " -0.000 2.00e-02 2.50e+03 pdb=" N9 ATP B 401 " -0.002 2.00e-02 2.50e+03 Histogram of nonbonded interaction distances: 2.03 - 2.61: 44 2.61 - 3.18: 2284 3.18 - 3.75: 2819 3.75 - 4.33: 5699 4.33 - 4.90: 10226 Nonbonded interactions: 21072 Sorted by model distance: nonbonded pdb=" N LEU B 240 " pdb=" N VAL B 241 " model vdw 2.034 2.560 nonbonded pdb=" N PHE D 83 " pdb=" N LEU D 84 " model vdw 2.040 2.560 nonbonded pdb=" N LEU A 58 " pdb=" N ASP A 59 " model vdw 2.065 2.560 nonbonded pdb=" N SER C 196 " pdb=" N GLU C 197 " model vdw 2.166 2.560 nonbonded pdb=" C LYS A 38 " pdb=" C GLU A 39 " model vdw 2.190 2.800 ... (remaining 21067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.020 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.160 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.190 ------------------------------------------------------------------------------- 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 : 6.696 70.879 1779 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.49 % Favored : 94.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.89 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 1758 helix: -0.92 (0.18), residues: 641 sheet: -0.01 (0.26), residues: 340 loop : -1.34 (0.21), residues: 777 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.877 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: 0.0470 time to fit residues: 4.9234 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 0.1980 chunk 73 optimal weight: 40.0000 chunk 45 optimal weight: 0.1980 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 chunk 83 optimal weight: 0.0570 chunk 102 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 overall best weight: 1.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3500 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.024 5415 Z= 0.081 Angle : 0.429 7.083 5438 Z= 0.253 Chirality : 0.041 0.074 8 Planarity : 0.001 0.002 2 Dihedral : 3.682 41.983 1779 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.33 % Favored : 97.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1758 helix: 1.29 (0.21), residues: 638 sheet: 0.55 (0.28), residues: 319 loop : -0.50 (0.22), residues: 801 *********************** 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 fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.854 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0464 time to fit residues: 4.9638 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 20.0000 chunk 49 optimal weight: 0.0970 chunk 132 optimal weight: 0.4980 chunk 108 optimal weight: 0.7980 chunk 43 optimal weight: 50.0000 chunk 159 optimal weight: 0.0670 chunk 171 optimal weight: 40.0000 chunk 141 optimal weight: 40.0000 chunk 157 optimal weight: 40.0000 chunk 54 optimal weight: 30.0000 chunk 127 optimal weight: 0.2980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3546 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.011 5415 Z= 0.038 Angle : 0.252 5.016 5438 Z= 0.144 Chirality : 0.026 0.052 8 Planarity : 0.000 0.000 2 Dihedral : 2.303 42.599 1779 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.45 % Favored : 97.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1758 helix: 2.89 (0.22), residues: 638 sheet: 1.01 (0.29), residues: 320 loop : -0.00 (0.22), residues: 800 *********************** 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 fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.873 Fit side-chains TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0461 time to fit residues: 4.8682 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 30.0000 chunk 119 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 50.0000 chunk 75 optimal weight: 30.0000 chunk 106 optimal weight: 0.4980 chunk 159 optimal weight: 0.9990 chunk 169 optimal weight: 50.0000 chunk 83 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 overall best weight: 10.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5203 moved from start: 1.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 5415 Z= 0.291 Angle : 0.954 10.992 5438 Z= 0.611 Chirality : 0.040 0.074 8 Planarity : 0.010 0.013 2 Dihedral : 8.379 89.890 1779 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.31 % Favored : 93.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1758 helix: -1.61 (0.20), residues: 506 sheet: -0.28 (0.32), residues: 253 loop : -0.52 (0.20), residues: 999 *********************** 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 fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.780 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: 0.0468 time to fit residues: 4.9113 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 5.9990 chunk 96 optimal weight: 0.0870 chunk 2 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 116 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 chunk 151 optimal weight: 8.9990 chunk 42 optimal weight: 30.0000 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 1.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 5415 Z= 0.173 Angle : 0.577 4.490 5438 Z= 0.378 Chirality : 0.034 0.064 8 Planarity : 0.004 0.004 2 Dihedral : 5.585 71.176 1779 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.35 % Favored : 94.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1758 helix: -1.25 (0.21), residues: 510 sheet: -0.21 (0.33), residues: 250 loop : -0.68 (0.20), residues: 998 *********************** 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 fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.847 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: 0.0466 time to fit residues: 4.9185 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 20.0000 chunk 152 optimal weight: 30.0000 chunk 33 optimal weight: 0.0770 chunk 99 optimal weight: 0.0000 chunk 41 optimal weight: 0.0980 chunk 169 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 78 optimal weight: 50.0000 chunk 14 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5274 moved from start: 1.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.013 5415 Z= 0.062 Angle : 0.322 4.102 5438 Z= 0.201 Chirality : 0.009 0.016 8 Planarity : 0.001 0.002 2 Dihedral : 3.695 51.045 1779 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.49 % Favored : 95.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1758 helix: -0.29 (0.22), residues: 544 sheet: -0.15 (0.33), residues: 253 loop : -0.51 (0.21), residues: 961 *********************** 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 fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.868 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: 0.0478 time to fit residues: 5.1756 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 40.0000 chunk 96 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 102 optimal weight: 50.0000 chunk 77 optimal weight: 0.0870 chunk 104 optimal weight: 0.2980 overall best weight: 6.6768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5611 moved from start: 1.9213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 5415 Z= 0.181 Angle : 0.633 5.097 5438 Z= 0.417 Chirality : 0.015 0.030 8 Planarity : 0.003 0.004 2 Dihedral : 6.223 56.409 1779 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.87 % Favored : 90.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1758 helix: -1.28 (0.23), residues: 427 sheet: -0.52 (0.36), residues: 201 loop : -0.94 (0.19), residues: 1130 *********************** 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 fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.857 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: 0.0463 time to fit residues: 4.9010 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 50.0000 chunk 100 optimal weight: 30.0000 chunk 50 optimal weight: 40.0000 chunk 33 optimal weight: 50.0000 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 50.0000 chunk 114 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 132 optimal weight: 9.9990 chunk 153 optimal weight: 40.0000 overall best weight: 18.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 2.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.090 5415 Z= 0.425 Angle : 1.213 16.716 5438 Z= 0.780 Chirality : 0.025 0.043 8 Planarity : 0.005 0.006 2 Dihedral : 9.713 59.173 1779 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 37.22 Ramachandran Plot: Outliers : 0.63 % Allowed : 17.12 % Favored : 82.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 1.25 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.18), residues: 1758 helix: -3.65 (0.18), residues: 379 sheet: -1.78 (0.49), residues: 92 loop : -2.41 (0.16), residues: 1287 *********************** 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 fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.850 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: 0.0470 time to fit residues: 5.0215 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 50.0000 chunk 147 optimal weight: 20.0000 chunk 157 optimal weight: 50.0000 chunk 94 optimal weight: 0.0770 chunk 68 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 156 optimal weight: 20.0000 chunk 103 optimal weight: 0.0270 overall best weight: 4.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 2.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 5415 Z= 0.120 Angle : 0.526 5.400 5438 Z= 0.335 Chirality : 0.015 0.024 8 Planarity : 0.001 0.001 2 Dihedral : 5.526 57.890 1779 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.75 % Favored : 89.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.18), residues: 1758 helix: -2.89 (0.20), residues: 412 sheet: -1.96 (0.41), residues: 133 loop : -2.04 (0.17), residues: 1213 *********************** 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 fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.887 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: 0.0494 time to fit residues: 5.3411 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 40.0000 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 174 optimal weight: 20.0000 chunk 160 optimal weight: 50.0000 chunk 138 optimal weight: 20.0000 chunk 14 optimal weight: 40.0000 chunk 107 optimal weight: 30.0000 chunk 85 optimal weight: 50.0000 chunk 110 optimal weight: 50.0000 overall best weight: 19.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 2.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.099 5415 Z= 0.433 Angle : 1.158 11.956 5438 Z= 0.750 Chirality : 0.038 0.070 8 Planarity : 0.006 0.007 2 Dihedral : 9.196 46.821 1779 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 43.34 Ramachandran Plot: Outliers : 1.14 % Allowed : 22.58 % Favored : 76.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 1.25 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.17), residues: 1758 helix: -3.88 (0.17), residues: 401 sheet: -1.89 (0.51), residues: 92 loop : -3.00 (0.16), residues: 1265 ********************** 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 fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.841 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: 0.0468 time to fit residues: 4.9095 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 128 optimal weight: 0.0070 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 50.0000 chunk 142 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 25 optimal weight: 50.0000 chunk 122 optimal weight: 4.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- 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 = 0.2993 r_free = 0.2993 target = 0.048339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.035771 restraints weight = 48181.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 13)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.035771 restraints weight = 50549.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.035771 restraints weight = 50549.517| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 2.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 5415 Z= 0.123 Angle : 0.553 7.927 5438 Z= 0.350 Chirality : 0.020 0.029 8 Planarity : 0.001 0.002 2 Dihedral : 5.698 49.442 1779 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.20 % Favored : 86.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.18), residues: 1758 helix: -3.07 (0.20), residues: 423 sheet: -2.15 (0.46), residues: 104 loop : -2.62 (0.17), residues: 1231 =============================================================================== Job complete usr+sys time: 1015.18 seconds wall clock time: 18 minutes 46.30 seconds (1126.30 seconds total)