Starting phenix.real_space_refine (version: dev) on Sat Feb 18 06:05:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_2023/7n9y_24264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_2023/7n9y_24264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_2023/7n9y_24264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_2023/7n9y_24264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_2023/7n9y_24264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_2023/7n9y_24264.pdb" } resolution = 4.8 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 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-4877/modules/chem_data/mon_lib" Total number of atoms: 7515 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 420 Classifications: {'peptide': 140} Incomplete info: {'n_c_alpha_c_only': 140} Link IDs: {'PTRANS': 13, 'TRANS': 126} Unresolved chain link angles: 152 Unresolved non-hydrogen bonds: 699 Unresolved non-hydrogen angles: 957 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 179 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 239 Chain: "A" Number of atoms: 7095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2365, 7095 Classifications: {'peptide': 2365} Incomplete info: {'n_c_alpha_c_only': 2365} Link IDs: {'CIS': 6, 'PTRANS': 52, 'TRANS': 2306} Chain breaks: 7 Unresolved chain link angles: 2416 Unresolved non-hydrogen bonds: 12299 Unresolved non-hydrogen angles: 16744 Unresolved non-hydrogen dihedrals: 6365 Unresolved non-hydrogen chiralities: 2907 Planarities with less than four sites: {'GLN:plan1': 59, 'HIS:plan': 23, 'TYR:plan': 134, 'ASN:plan1': 194, 'TRP:plan': 16, 'ASP:plan': 182, 'PHE:plan': 132, 'GLU:plan': 210, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 5119 Residues with excluded nonbonded symmetry interactions: 1674 residue: pdb=" N SER A 2 " occ=0.00 pdb=" CA SER A 2 " occ=0.00 pdb=" C SER A 2 " occ=0.00 residue: pdb=" N LEU A 3 " occ=0.00 pdb=" CA LEU A 3 " occ=0.00 pdb=" C LEU A 3 " occ=0.00 residue: pdb=" N VAL A 4 " occ=0.00 pdb=" CA VAL A 4 " occ=0.00 pdb=" C VAL A 4 " occ=0.00 residue: pdb=" N ASN A 5 " occ=0.00 pdb=" CA ASN A 5 " occ=0.00 pdb=" C ASN A 5 " occ=0.00 residue: pdb=" N ARG A 6 " occ=0.00 pdb=" CA ARG A 6 " occ=0.00 pdb=" C ARG A 6 " occ=0.00 residue: pdb=" N LYS A 7 " occ=0.00 pdb=" CA LYS A 7 " occ=0.00 pdb=" C LYS A 7 " occ=0.00 residue: pdb=" N GLN A 8 " occ=0.00 pdb=" CA GLN A 8 " occ=0.00 pdb=" C GLN A 8 " occ=0.00 residue: pdb=" N LEU A 9 " occ=0.00 pdb=" CA LEU A 9 " occ=0.00 pdb=" C LEU A 9 " occ=0.00 residue: pdb=" N GLU A 10 " occ=0.00 pdb=" CA GLU A 10 " occ=0.00 pdb=" C GLU A 10 " occ=0.00 residue: pdb=" N LYS A 11 " occ=0.00 pdb=" CA LYS A 11 " occ=0.00 pdb=" C LYS A 11 " occ=0.00 residue: pdb=" N MET A 12 " occ=0.00 pdb=" CA MET A 12 " occ=0.00 pdb=" C MET A 12 " occ=0.00 residue: pdb=" N ALA A 13 " occ=0.00 pdb=" CA ALA A 13 " occ=0.00 pdb=" C ALA A 13 " occ=0.00 ... (remaining 1662 not shown) Time building chain proxies: 5.86, per 1000 atoms: 0.78 Number of scatterers: 7515 At special positions: 0 Unit cell: (144.64, 136.73, 241.82, 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 2505 7.00 C 5010 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: 1.98 Conformation dependent library (CDL) restraints added in 2.5 seconds 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 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: 2.77 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: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.32 - 1.64: 7504 1.64 - 1.96: 1 1.96 - 2.28: 0 2.28 - 2.60: 0 2.60 - 2.92: 1 Bond restraints: 7506 Sorted by residual: bond pdb=" C TRP A1742 " pdb=" N SER A1743 " ideal model delta sigma weight residual 1.332 2.920 -1.587 1.40e-02 5.10e+03 1.29e+04 bond pdb=" CA ASN A 422 " pdb=" C ASN A 422 " ideal model delta sigma weight residual 1.526 1.865 -0.338 1.03e-02 9.43e+03 1.08e+03 bond pdb=" C ASN A 422 " pdb=" N ASP A 423 " ideal model delta sigma weight residual 1.331 1.398 -0.067 1.36e-02 5.41e+03 2.42e+01 bond pdb=" N ASN A 422 " pdb=" CA ASN A 422 " ideal model delta sigma weight residual 1.463 1.492 -0.029 1.27e-02 6.20e+03 5.21e+00 bond pdb=" N ASP A 614 " pdb=" CA ASP A 614 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.86e+00 ... (remaining 7501 not shown) Histogram of bond angle deviations from ideal: 89.45 - 97.44: 1 97.44 - 105.43: 2 105.43 - 113.42: 2364 113.42 - 121.41: 3713 121.41 - 129.40: 1417 Bond angle restraints: 7497 Sorted by residual: angle pdb=" CA TRP A1742 " pdb=" C TRP A1742 " pdb=" N SER A1743 " ideal model delta sigma weight residual 116.29 89.45 26.84 1.30e+00 5.92e-01 4.26e+02 angle pdb=" C TRP A1742 " pdb=" N SER A1743 " pdb=" CA SER A1743 " ideal model delta sigma weight residual 121.54 97.82 23.72 1.91e+00 2.74e-01 1.54e+02 angle pdb=" CA ASN A 422 " pdb=" C ASN A 422 " pdb=" N ASP A 423 " ideal model delta sigma weight residual 116.26 126.63 -10.37 1.27e+00 6.20e-01 6.67e+01 angle pdb=" N ASN A 422 " pdb=" CA ASN A 422 " pdb=" C ASN A 422 " ideal model delta sigma weight residual 107.23 119.24 -12.01 1.67e+00 3.59e-01 5.17e+01 angle pdb=" N ILE A1085 " pdb=" CA ILE A1085 " pdb=" C ILE A1085 " ideal model delta sigma weight residual 113.71 108.66 5.05 9.50e-01 1.11e+00 2.83e+01 ... (remaining 7492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.23: 1836 6.23 - 12.46: 536 12.46 - 18.69: 106 18.69 - 24.92: 16 24.92 - 31.15: 2 Dihedral angle restraints: 2496 sinusoidal: 0 harmonic: 2496 Sorted by residual: dihedral pdb=" CA ASP A 421 " pdb=" C ASP A 421 " pdb=" N ASN A 422 " pdb=" CA ASN A 422 " ideal model delta harmonic sigma weight residual 180.00 148.85 31.15 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA THR A1713 " pdb=" C THR A1713 " pdb=" N TYR A1714 " pdb=" CA TYR A1714 " ideal model delta harmonic sigma weight residual 180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLU A1947 " pdb=" C GLU A1947 " pdb=" N TRP A1948 " pdb=" CA TRP A1948 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 2493 not shown) Chirality restraints: 0 Planarity restraints: 0 Histogram of nonbonded interaction distances: 2.54 - 3.01: 1577 3.01 - 3.48: 2974 3.48 - 3.96: 5393 3.96 - 4.43: 6288 4.43 - 4.90: 10995 Nonbonded interactions: 27227 Sorted by model distance: nonbonded pdb=" N ARG A 165 " pdb=" N PHE A 166 " model vdw 2.538 2.560 nonbonded pdb=" N GLU A 904 " pdb=" N THR A 905 " model vdw 2.562 2.560 nonbonded pdb=" N ASN A1941 " pdb=" N TYR A1942 " model vdw 2.571 2.560 nonbonded pdb=" N SER A 881 " pdb=" N HIS A 882 " model vdw 2.577 2.560 nonbonded pdb=" N ILE A1193 " pdb=" N THR A1194 " model vdw 2.577 2.560 ... (remaining 27222 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 5010 2.51 5 N 2505 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=0.00 max=1.00 mean=0.33 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.960 Check model and map are aligned: 0.110 Process input model: 22.310 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3255 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 : 0.019 1.587 7506 Z= 1.377 Angle : 1.072 26.844 7497 Z= 0.723 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.040 31.146 2496 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.53 % Favored : 91.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.98 (0.16), residues: 2485 helix: -0.12 (0.21), residues: 558 sheet: -1.32 (0.27), residues: 354 loop : -1.84 (0.15), residues: 1573 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.285 Fit side-chains TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it. 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: 47 average time/residue: 0.0628 time to fit residues: 7.3841 Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 105 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 127 optimal weight: 0.3980 chunk 101 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 119 optimal weight: 0.0470 chunk 145 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 overall best weight: 1.5680 ------------------------------------------------------------------------------- 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: 0.3452 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 7506 Z= 0.277 Angle : 0.794 10.551 7497 Z= 0.504 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.221 30.254 2496 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.09 % Favored : 90.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.18 (0.16), residues: 2487 helix: -0.47 (0.23), residues: 467 sheet: -0.93 (0.33), residues: 249 loop : -1.94 (0.14), residues: 1771 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.951 Fit side-chains TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it. 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: 47 average time/residue: 0.0635 time to fit residues: 7.3250 Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 245 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 182 optimal weight: 0.0270 overall best weight: 4.2046 ------------------------------------------------------------------------------- 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: 0.3460 moved from start: 1.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.083 7506 Z= 0.531 Angle : 1.380 15.021 7497 Z= 0.884 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 9.593 36.607 2496 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 24.67 Ramachandran Plot: Outliers : 1.01 % Allowed : 15.68 % Favored : 83.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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 (0.15), residues: 2487 helix: -3.48 (0.18), residues: 365 sheet: -2.10 (0.33), residues: 213 loop : -2.61 (0.13), residues: 1909 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.139 Fit side-chains TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it. 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: 47 average time/residue: 0.0679 time to fit residues: 7.9650 Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 6.9990 chunk 170 optimal weight: 0.0870 chunk 118 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 108 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 65 optimal weight: 0.0170 overall best weight: 2.2202 ------------------------------------------------------------------------------- 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: 0.3394 moved from start: 1.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7506 Z= 0.288 Angle : 0.848 10.376 7497 Z= 0.542 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.686 33.215 2496 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.36 % Allowed : 16.20 % Favored : 83.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.89 (0.15), residues: 2487 helix: -3.38 (0.18), residues: 415 sheet: -2.25 (0.33), residues: 208 loop : -2.64 (0.13), residues: 1864 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.187 Fit side-chains TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it. 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: 47 average time/residue: 0.0663 time to fit residues: 7.8911 Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 3 optimal weight: 0.0070 chunk 179 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 60 optimal weight: 0.0060 overall best weight: 3.4020 ------------------------------------------------------------------------------- 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: 0.3397 moved from start: 1.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 7506 Z= 0.434 Angle : 1.134 10.979 7497 Z= 0.725 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.506 34.667 2496 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.72 % Allowed : 22.16 % Favored : 77.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.48 (0.14), residues: 2487 helix: -3.92 (0.17), residues: 350 sheet: -2.42 (0.36), residues: 191 loop : -3.14 (0.12), residues: 1946 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.213 Fit side-chains TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it. 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: 47 average time/residue: 0.0699 time to fit residues: 8.3226 Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 0.0010 chunk 217 optimal weight: 10.0000 chunk 47 optimal weight: 0.0370 chunk 141 optimal weight: 7.9990 chunk 59 optimal weight: 0.0970 chunk 241 optimal weight: 2.9990 chunk 200 optimal weight: 0.3980 chunk 111 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 overall best weight: 0.2262 ------------------------------------------------------------------------------- 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: 0.3271 moved from start: 1.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.011 7506 Z= 0.067 Angle : 0.443 6.428 7497 Z= 0.271 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.084 23.192 2496 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.77 % Favored : 89.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -3.71 (0.15), residues: 2487 helix: -2.50 (0.21), residues: 411 sheet: -1.92 (0.38), residues: 208 loop : -2.75 (0.13), residues: 1868 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.092 Fit side-chains TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it. 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: 47 average time/residue: 0.0662 time to fit residues: 7.5765 Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 111 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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: 0.3433 moved from start: 1.7360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.100 7506 Z= 0.658 Angle : 1.511 11.423 7497 Z= 0.988 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 9.874 36.731 2496 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 46.66 Ramachandran Plot: Outliers : 2.17 % Allowed : 26.34 % Favored : 71.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 1.54 % Twisted General : 0.58 % 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: -4.98 (0.14), residues: 2487 helix: -4.30 (0.16), residues: 335 sheet: -2.64 (0.42), residues: 145 loop : -3.52 (0.12), residues: 2007 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.009 Fit side-chains TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it. 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: 47 average time/residue: 0.0632 time to fit residues: 7.3493 Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 72 optimal weight: 0.0020 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 119 optimal weight: 0.0270 chunk 22 optimal weight: 0.4980 chunk 189 optimal weight: 10.0000 overall best weight: 0.4648 ------------------------------------------------------------------------------- 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: 0.3272 moved from start: 1.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.017 7506 Z= 0.092 Angle : 0.509 5.034 7497 Z= 0.317 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.762 24.882 2496 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.63 % Favored : 87.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -4.30 (0.15), residues: 2487 helix: -3.04 (0.21), residues: 382 sheet: -2.31 (0.39), residues: 192 loop : -3.16 (0.13), residues: 1913 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.062 Fit side-chains TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it. 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: 47 average time/residue: 0.0666 time to fit residues: 7.6730 Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 219 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 97 optimal weight: 0.0000 chunk 176 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- 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: 0.3385 moved from start: 1.7753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 7506 Z= 0.437 Angle : 1.116 8.654 7497 Z= 0.725 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.180 32.573 2496 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.76 % Allowed : 27.18 % Favored : 72.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.72 (0.15), residues: 2487 helix: -4.02 (0.18), residues: 312 sheet: -2.41 (0.41), residues: 171 loop : -3.38 (0.12), residues: 2004 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.118 Fit side-chains TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it. 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: 47 average time/residue: 0.0690 time to fit residues: 8.1425 Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 147 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 112 optimal weight: 0.0670 chunk 165 optimal weight: 10.0000 chunk 249 optimal weight: 0.0470 chunk 229 optimal weight: 0.0030 chunk 198 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 0.0670 overall best weight: 0.6366 ------------------------------------------------------------------------------- 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: 0.3274 moved from start: 1.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.023 7506 Z= 0.104 Angle : 0.496 4.834 7497 Z= 0.311 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.678 25.441 2496 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.99 % Favored : 86.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -4.27 (0.15), residues: 2487 helix: -2.77 (0.22), residues: 393 sheet: -2.03 (0.41), residues: 181 loop : -3.22 (0.13), residues: 1913 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.992 Fit side-chains TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it. 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: 47 average time/residue: 0.0637 time to fit residues: 7.2966 Evaluate side-chains 47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 0.0970 chunk 211 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 83 optimal weight: 0.0470 chunk 203 optimal weight: 9.9990 chunk 25 optimal weight: 0.0270 chunk 36 optimal weight: 5.9990 overall best weight: 0.8336 ------------------------------------------------------------------------------- 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 = 0.4802 r_free = 0.4802 target = 0.276509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.262438 restraints weight = 36579.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.262438 restraints weight = 37377.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.262438 restraints weight = 37378.732| |-----------------------------------------------------------------------------| r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3064 moved from start: 1.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7506 Z= 0.120 Angle : 0.481 4.747 7497 Z= 0.304 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.449 25.596 2496 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.36 % Allowed : 19.38 % Favored : 80.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -4.00 (0.15), residues: 2487 helix: -2.33 (0.24), residues: 379 sheet: -2.04 (0.40), residues: 189 loop : -3.07 (0.13), residues: 1919 =============================================================================== Job complete usr+sys time: 1457.89 seconds wall clock time: 26 minutes 51.87 seconds (1611.87 seconds total)