Starting phenix.real_space_refine on Wed Feb 12 08:40:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n9y_24264/02_2025/7n9y_24264.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n9y_24264/02_2025/7n9y_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/cci-nas-00/data/ceres_data/7n9y_24264/02_2025/7n9y_24264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n9y_24264/02_2025/7n9y_24264.map" model { file = "/net/cci-nas-00/data/ceres_data/7n9y_24264/02_2025/7n9y_24264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n9y_24264/02_2025/7n9y_24264.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.29, per 1000 atoms: 0.97 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.7 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: 3.45 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: 2.06 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: 0.00 - 5.37: 7481 5.37 - 10.74: 13 10.74 - 16.11: 1 16.11 - 21.48: 0 21.48 - 26.84: 2 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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.020 Set scattering table: 0.070 Process input model: 22.240 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3280 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 : 1.073 26.844 7497 Z= 0.724 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 % Allowed : 0.00 % Favored : 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.078 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: 0.0648 time to fit residues: 7.6390 Evaluate side-chains 47 residues out of total 2259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.274272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.258432 restraints weight = 33459.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.258144 restraints weight = 35543.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.258144 restraints weight = 37897.978| |-----------------------------------------------------------------------------| r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3331 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7506 Z= 0.218 Angle : 0.787 11.928 7497 Z= 0.498 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.090 29.069 2496 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.97 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -2.14 (0.16), residues: 2487 helix: -0.45 (0.23), residues: 478 sheet: -0.89 (0.34), residues: 255 loop : -1.91 (0.14), residues: 1754 *********************** 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.946 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: 0.0658 time to fit residues: 7.5001 Evaluate side-chains 47 residues out of total 2259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 140 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 44 optimal weight: 0.0020 chunk 163 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4793 r_free = 0.4793 target = 0.274510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.259696 restraints weight = 35550.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.259679 restraints weight = 37031.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.259679 restraints weight = 37266.455| |-----------------------------------------------------------------------------| r_work (final): 0.4591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3270 moved from start: 0.9695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7506 Z= 0.243 Angle : 0.790 6.016 7497 Z= 0.509 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.312 28.698 2496 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.86 % Favored : 88.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -2.71 (0.15), residues: 2487 helix: -1.30 (0.23), residues: 439 sheet: -1.34 (0.31), residues: 267 loop : -2.15 (0.14), residues: 1781 *********************** 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.130 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: 0.0664 time to fit residues: 7.8381 Evaluate side-chains 47 residues out of total 2259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 202 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 204 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 151 optimal weight: 0.0060 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.7002 ------------------------------------------------------------------------------- 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 = 0.4795 r_free = 0.4795 target = 0.274879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.260251 restraints weight = 35946.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.260251 restraints weight = 37153.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.260251 restraints weight = 37153.988| |-----------------------------------------------------------------------------| r_work (final): 0.4590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3223 moved from start: 1.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7506 Z= 0.231 Angle : 0.738 11.063 7497 Z= 0.469 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.897 27.753 2496 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.98 % Favored : 87.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -2.91 (0.16), residues: 2487 helix: -1.68 (0.23), residues: 438 sheet: -1.63 (0.30), residues: 275 loop : -2.20 (0.14), residues: 1774 *********************** 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.047 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: 0.0630 time to fit residues: 7.2764 Evaluate side-chains 47 residues out of total 2259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 129 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 135 optimal weight: 0.0050 chunk 207 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.2800 ------------------------------------------------------------------------------- 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 = 0.4778 r_free = 0.4778 target = 0.274319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.260530 restraints weight = 37051.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.260388 restraints weight = 37884.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.260383 restraints weight = 38756.617| |-----------------------------------------------------------------------------| r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3202 moved from start: 1.3872 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 : 0.870 8.894 7497 Z= 0.558 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.864 29.317 2496 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.52 % Favored : 84.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -3.66 (0.15), residues: 2487 helix: -2.96 (0.20), residues: 413 sheet: -2.00 (0.33), residues: 221 loop : -2.56 (0.13), residues: 1853 *********************** 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.031 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: 0.0680 time to fit residues: 7.7916 Evaluate side-chains 47 residues out of total 2259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 204 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 47 optimal weight: 0.0010 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 98 optimal weight: 50.0000 chunk 180 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- 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 = 0.4771 r_free = 0.4771 target = 0.273888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.260656 restraints weight = 38151.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.260592 restraints weight = 38793.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.260482 restraints weight = 39416.309| |-----------------------------------------------------------------------------| r_work (final): 0.4575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3202 moved from start: 1.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 7506 Z= 0.385 Angle : 1.041 12.392 7497 Z= 0.669 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.840 32.322 2496 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.60 % Allowed : 19.10 % Favored : 80.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.33 (0.14), residues: 2487 helix: -3.79 (0.18), residues: 364 sheet: -2.26 (0.38), residues: 181 loop : -3.03 (0.12), residues: 1942 *********************** 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.106 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: 0.0645 time to fit residues: 7.3503 Evaluate side-chains 47 residues out of total 2259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 chunk 162 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 = 0.4764 r_free = 0.4764 target = 0.273985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.261034 restraints weight = 38685.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.260914 restraints weight = 39248.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.260914 restraints weight = 40027.758| |-----------------------------------------------------------------------------| r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3177 moved from start: 1.7297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 7506 Z= 0.428 Angle : 1.116 11.610 7497 Z= 0.721 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.266 34.664 2496 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 26.75 Ramachandran Plot: Outliers : 0.60 % Allowed : 22.92 % Favored : 76.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.59 (0.14), residues: 2487 helix: -3.93 (0.18), residues: 351 sheet: -2.51 (0.40), residues: 158 loop : -3.23 (0.12), residues: 1978 *********************** 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.044 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: 0.0672 time to fit residues: 7.7708 Evaluate side-chains 47 residues out of total 2259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 95 optimal weight: 0.0040 chunk 27 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 206 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 86 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- 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 = 0.4786 r_free = 0.4786 target = 0.275253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.261714 restraints weight = 37631.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.261673 restraints weight = 38188.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.261673 restraints weight = 38671.515| |-----------------------------------------------------------------------------| r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3128 moved from start: 1.7127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7506 Z= 0.222 Angle : 0.717 7.375 7497 Z= 0.462 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.070 26.320 2496 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.44 % Allowed : 18.86 % Favored : 80.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -4.59 (0.14), residues: 2487 helix: -3.65 (0.17), residues: 409 sheet: -2.43 (0.38), residues: 178 loop : -3.26 (0.12), residues: 1900 *********************** 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.059 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: 0.0673 time to fit residues: 7.9954 Evaluate side-chains 47 residues out of total 2259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 12 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 42 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 63 optimal weight: 0.4980 overall best weight: 3.6586 ------------------------------------------------------------------------------- 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 = 0.4761 r_free = 0.4761 target = 0.273821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.260934 restraints weight = 40220.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.260933 restraints weight = 40602.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.260933 restraints weight = 40602.328| |-----------------------------------------------------------------------------| r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3177 moved from start: 1.8531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 7506 Z= 0.438 Angle : 1.126 9.785 7497 Z= 0.730 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.274 35.991 2496 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 27.93 Ramachandran Plot: Outliers : 0.64 % Allowed : 26.90 % Favored : 72.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.14), residues: 2487 helix: -3.97 (0.18), residues: 352 sheet: -2.20 (0.40), residues: 170 loop : -3.53 (0.12), residues: 1965 *********************** 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.130 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: 0.0687 time to fit residues: 8.3283 Evaluate side-chains 47 residues out of total 2259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4780 r_free = 0.4780 target = 0.275061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.261714 restraints weight = 38597.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.261714 restraints weight = 39018.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.261714 restraints weight = 39018.272| |-----------------------------------------------------------------------------| r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3105 moved from start: 1.8414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7506 Z= 0.270 Angle : 0.805 7.533 7497 Z= 0.518 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.579 30.863 2496 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.48 % Allowed : 20.79 % Favored : 78.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -4.80 (0.14), residues: 2487 helix: -3.88 (0.17), residues: 383 sheet: -2.07 (0.43), residues: 157 loop : -3.46 (0.12), residues: 1947 ********************** 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.103 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: 0.0627 time to fit residues: 7.3542 Evaluate side-chains 47 residues out of total 2259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 222 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 186 optimal weight: 6.9990 chunk 19 optimal weight: 0.0370 chunk 12 optimal weight: 8.9990 chunk 121 optimal weight: 0.0980 chunk 62 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 0.0270 overall best weight: 2.0320 ------------------------------------------------------------------------------- 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 = 0.4779 r_free = 0.4779 target = 0.275035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.261742 restraints weight = 38494.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.261701 restraints weight = 39147.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.261701 restraints weight = 39556.029| |-----------------------------------------------------------------------------| r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3109 moved from start: 1.8942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7506 Z= 0.254 Angle : 0.785 7.758 7497 Z= 0.505 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.483 32.928 2496 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.48 % Allowed : 26.46 % Favored : 73.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -4.83 (0.14), residues: 2487 helix: -3.67 (0.18), residues: 393 sheet: -2.28 (0.40), residues: 175 loop : -3.52 (0.13), residues: 1919 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2110.50 seconds wall clock time: 37 minutes 55.27 seconds (2275.27 seconds total)