Starting phenix.real_space_refine (version: dev) on Thu May 12 17:45:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/05_2022/7n9q_24259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/05_2022/7n9q_24259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/05_2022/7n9q_24259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/05_2022/7n9q_24259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/05_2022/7n9q_24259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/05_2022/7n9q_24259.pdb" } resolution = 4.6 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= 0.001 sd= 0.019 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 6945 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2315, 6945 Classifications: {'peptide': 2315} Incomplete info: {'n_c_alpha_c_only': 2315} Link IDs: {'PTRANS': 49, 'TRANS': 2264, 'PCIS': 1} Chain breaks: 2 Unresolved chain link angles: 2364 Unresolved non-hydrogen bonds: 12079 Unresolved non-hydrogen angles: 16444 Unresolved non-hydrogen dihedrals: 6273 Unresolved non-hydrogen chiralities: 2840 Planarities with less than four sites: {'GLN:plan1': 58, 'HIS:plan': 23, 'TYR:plan': 134, 'ASN:plan1': 192, 'TRP:plan': 16, 'ASP:plan': 180, 'PHE:plan': 132, 'GLU:plan': 205, 'ARG:plan': 48} Unresolved non-hydrogen planarities: 5074 Time building chain proxies: 5.47, per 1000 atoms: 0.79 Number of scatterers: 6945 At special positions: 0 Unit cell: (134.703, 146.37, 256.677, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 2 Type Number sf(0) N 2315 7.00 C 4630 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: 1.70 Conformation dependent library (CDL) restraints added in 2.1 seconds 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 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: 2.57 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: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.32 - 1.36: 2312 1.36 - 1.41: 0 1.41 - 1.45: 123 1.45 - 1.50: 2192 1.50 - 1.54: 2315 Bond restraints: 6942 Sorted by residual: bond pdb=" CA VAL A1094 " pdb=" C VAL A1094 " ideal model delta sigma weight residual 1.525 1.540 -0.015 8.80e-03 1.29e+04 2.76e+00 bond pdb=" N ASP A 442 " pdb=" CA ASP A 442 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.54e+00 bond pdb=" CA ASP A1500 " pdb=" C ASP A1500 " ideal model delta sigma weight residual 1.523 1.532 -0.009 8.40e-03 1.42e+04 1.04e+00 bond pdb=" N ASN A1839 " pdb=" CA ASN A1839 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.99e-01 bond pdb=" N SER A1242 " pdb=" CA SER A1242 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.78e-01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 105.27 - 110.81: 1225 110.81 - 116.35: 2113 116.35 - 121.89: 2570 121.89 - 127.43: 1022 127.43 - 132.97: 9 Bond angle restraints: 6939 Sorted by residual: angle pdb=" C ALA A 441 " pdb=" N ASP A 442 " pdb=" CA ASP A 442 " ideal model delta sigma weight residual 121.54 132.97 -11.43 1.91e+00 2.74e-01 3.58e+01 angle pdb=" C PHE A2069 " pdb=" N ASP A2070 " pdb=" CA ASP A2070 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C GLN A 193 " pdb=" N ARG A 194 " pdb=" CA ARG A 194 " ideal model delta sigma weight residual 121.58 112.24 9.34 1.95e+00 2.63e-01 2.29e+01 angle pdb=" N TYR A2223 " pdb=" CA TYR A2223 " pdb=" C TYR A2223 " ideal model delta sigma weight residual 114.75 109.14 5.61 1.26e+00 6.30e-01 1.98e+01 angle pdb=" C LYS A 76 " pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta sigma weight residual 120.31 114.02 6.29 1.52e+00 4.33e-01 1.71e+01 ... (remaining 6934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.68: 1687 5.68 - 11.36: 505 11.36 - 17.04: 98 17.04 - 22.71: 19 22.71 - 28.39: 3 Dihedral angle restraints: 2312 sinusoidal: 0 harmonic: 2312 Sorted by residual: dihedral pdb=" CA TYR A2213 " pdb=" C TYR A2213 " pdb=" N ASP A2214 " pdb=" CA ASP A2214 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA THR A1234 " pdb=" C THR A1234 " pdb=" N GLY A1235 " pdb=" CA GLY A1235 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA GLU A1212 " pdb=" C GLU A1212 " pdb=" N LEU A1213 " pdb=" CA LEU A1213 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 2309 not shown) Chirality restraints: 0 Planarity restraints: 0 Histogram of nonbonded interaction distances: 2.60 - 3.06: 1995 3.06 - 3.52: 2446 3.52 - 3.98: 4853 3.98 - 4.44: 6241 4.44 - 4.90: 9761 Nonbonded interactions: 25296 Sorted by model distance: nonbonded pdb=" N ASP A 442 " pdb=" N ASN A 443 " model vdw 2.600 2.560 nonbonded pdb=" N ASP A1812 " pdb=" N LEU A1813 " model vdw 2.603 2.560 nonbonded pdb=" N ILE A1809 " pdb=" N GLY A1810 " model vdw 2.606 2.560 nonbonded pdb=" N ASP A2214 " pdb=" N MET A2215 " model vdw 2.618 2.560 nonbonded pdb=" N GLY A1088 " pdb=" N PHE A1089 " model vdw 2.627 2.560 ... (remaining 25291 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 Set scattering table Set to: electron Number of scattering types: 2 Type Number sf(0) Gaussians C 4630 2.51 5 N 2315 2.21 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.710 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: 17.610 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 20.540 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.002 0.016 6942 Z= 0.171 Angle : 0.883 11.435 6939 Z= 0.561 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.650 28.393 2312 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.78 % Allowed : 8.92 % Favored : 90.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2309 helix: 0.26 (0.21), residues: 569 sheet: -0.42 (0.26), residues: 374 loop : -1.90 (0.16), residues: 1366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.142 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0619 time to fit residues: 6.7834 Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 6.9990 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 93 optimal weight: 0.0020 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 0.0570 chunk 110 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 overall best weight: 0.8708 ------------------------------------------------------------------------------- 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: 0.7371 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 6942 Z= 0.126 Angle : 0.520 5.275 6939 Z= 0.326 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.362 22.589 2312 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.49 % Favored : 91.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2309 helix: 1.56 (0.22), residues: 547 sheet: -0.54 (0.25), residues: 410 loop : -1.81 (0.16), residues: 1352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.061 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0589 time to fit residues: 6.6915 Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 227 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 chunk 71 optimal weight: 0.4980 chunk 168 optimal weight: 2.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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: 0.7703 moved from start: 0.7802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6942 Z= 0.248 Angle : 0.862 8.767 6939 Z= 0.539 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.490 26.803 2312 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.74 % Allowed : 10.57 % Favored : 88.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2309 helix: -0.02 (0.25), residues: 418 sheet: -1.10 (0.27), residues: 362 loop : -1.96 (0.15), residues: 1529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.035 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0592 time to fit residues: 6.6430 Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 110 optimal weight: 0.0670 chunk 199 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- 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: 0.7752 moved from start: 0.9247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6942 Z= 0.214 Angle : 0.735 10.626 6939 Z= 0.458 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.621 20.543 2312 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.57 % Favored : 88.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.16), residues: 2309 helix: -0.33 (0.27), residues: 367 sheet: -1.25 (0.29), residues: 320 loop : -2.12 (0.14), residues: 1622 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.114 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0599 time to fit residues: 6.8497 Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.8015 moved from start: 1.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.112 6942 Z= 0.581 Angle : 1.571 26.012 6939 Z= 0.979 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 10.253 38.117 2312 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 45.92 Ramachandran Plot: Outliers : 1.39 % Allowed : 20.44 % Favored : 78.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.40 % 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: -4.17 (0.15), residues: 2309 helix: -3.21 (0.22), residues: 305 sheet: -1.85 (0.31), residues: 257 loop : -3.10 (0.13), residues: 1747 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.977 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0602 time to fit residues: 6.7861 Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.8070 moved from start: 1.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.086 6942 Z= 0.579 Angle : 1.485 15.156 6939 Z= 0.939 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 10.041 43.952 2312 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 50.35 Ramachandran Plot: Outliers : 1.13 % Allowed : 23.99 % Favored : 74.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -4.66 (0.15), residues: 2309 helix: -3.94 (0.19), residues: 305 sheet: -1.87 (0.37), residues: 207 loop : -3.41 (0.13), residues: 1797 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.931 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0562 time to fit residues: 6.3262 Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8021 moved from start: 1.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 6942 Z= 0.272 Angle : 0.911 9.306 6939 Z= 0.577 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.579 28.735 2312 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.87 % Allowed : 21.18 % Favored : 77.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.15), residues: 2309 helix: -3.47 (0.22), residues: 301 sheet: -2.01 (0.35), residues: 232 loop : -3.33 (0.13), residues: 1776 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.007 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0581 time to fit residues: 6.5550 Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 141 optimal weight: 0.4980 chunk 151 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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: 0.8044 moved from start: 1.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 6942 Z= 0.308 Angle : 0.952 9.670 6939 Z= 0.611 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.727 34.743 2312 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 30.61 Ramachandran Plot: Outliers : 0.87 % Allowed : 26.07 % Favored : 73.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.62 (0.15), residues: 2309 helix: -3.42 (0.23), residues: 302 sheet: -1.95 (0.36), residues: 229 loop : -3.48 (0.13), residues: 1778 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.032 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0616 time to fit residues: 6.8688 Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 7.9990 chunk 194 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 162 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.8107 moved from start: 1.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.078 6942 Z= 0.512 Angle : 1.345 12.075 6939 Z= 0.864 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 9.323 51.696 2312 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 46.87 Ramachandran Plot: Outliers : 1.04 % Allowed : 29.45 % Favored : 69.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.14), residues: 2309 helix: -3.77 (0.21), residues: 287 sheet: -1.73 (0.48), residues: 143 loop : -3.81 (0.12), residues: 1879 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.089 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0605 time to fit residues: 6.8003 Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 230 optimal weight: 40.0000 chunk 211 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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: 0.8081 moved from start: 1.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 6942 Z= 0.369 Angle : 1.052 10.216 6939 Z= 0.680 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.082 44.420 2312 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 34.41 Ramachandran Plot: Outliers : 0.95 % Allowed : 27.54 % Favored : 71.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.15), residues: 2309 helix: -3.38 (0.24), residues: 275 sheet: -2.20 (0.42), residues: 177 loop : -3.82 (0.12), residues: 1857 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.097 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0608 time to fit residues: 6.8139 Evaluate side-chains 44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 5.9990 chunk 56 optimal weight: 0.0270 chunk 168 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 76 optimal weight: 0.0370 chunk 188 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 0.0570 chunk 161 optimal weight: 7.9990 overall best weight: 0.3634 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.104090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.058764 restraints weight = 17567.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.057826 restraints weight = 20059.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.057177 restraints weight = 22275.510| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 1.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.018 6942 Z= 0.090 Angle : 0.484 5.629 6939 Z= 0.311 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.013 26.621 2312 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.87 % Allowed : 13.17 % Favored : 85.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.15), residues: 2309 helix: -2.52 (0.25), residues: 341 sheet: -2.40 (0.38), residues: 198 loop : -3.48 (0.13), residues: 1770 =============================================================================== Job complete usr+sys time: 1489.40 seconds wall clock time: 27 minutes 10.31 seconds (1630.31 seconds total)