Starting phenix.real_space_refine on Wed Sep 17 08:54:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n95_24250/09_2025/7n95_24250.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n95_24250/09_2025/7n95_24250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n95_24250/09_2025/7n95_24250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n95_24250/09_2025/7n95_24250.map" model { file = "/net/cci-nas-00/data/ceres_data/7n95_24250/09_2025/7n95_24250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n95_24250/09_2025/7n95_24250.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 4866 2.51 5 N 2433 2.21 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7299 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 363 Classifications: {'peptide': 121} Incomplete info: {'n_c_alpha_c_only': 121} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 110} Unresolved chain link angles: 130 Unresolved non-hydrogen bonds: 629 Unresolved non-hydrogen angles: 854 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 141 Planarities with less than four sites: {'ASP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 7, 'GLN:plan1': 10, 'TYR:plan': 3, 'ASN:plan1': 5, 'GLU:plan': 9, 'ARG:plan': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 262 Chain: "A" Number of atoms: 6936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2312, 6936 Classifications: {'peptide': 2312} Incomplete info: {'n_c_alpha_c_only': 2312} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 2262} Chain breaks: 2 Unresolved chain link angles: 2360 Unresolved non-hydrogen bonds: 12070 Unresolved non-hydrogen angles: 16430 Unresolved non-hydrogen dihedrals: 6269 Unresolved non-hydrogen chiralities: 2838 Planarities with less than four sites: {'ASN:plan1': 192, 'ARG:plan': 47, 'GLN:plan1': 58, 'GLU:plan': 207, 'PHE:plan': 131, 'ASP:plan': 179, 'TYR:plan': 134, 'HIS:plan': 23, 'TRP:plan': 16} Unresolved non-hydrogen planarities: 5066 Time building chain proxies: 2.60, per 1000 atoms: 0.36 Number of scatterers: 7299 At special positions: 0 Unit cell: (132.581, 145.309, 255.617, 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 2433 7.00 C 4866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 568.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.32 - 1.36: 2429 1.36 - 1.41: 0 1.41 - 1.45: 256 1.45 - 1.50: 2177 1.50 - 1.54: 2433 Bond restraints: 7295 Sorted by residual: bond pdb=" CA THR A2204 " pdb=" C THR A2204 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.56e-02 4.11e+03 1.91e+00 bond pdb=" N ASP A2145 " pdb=" CA ASP A2145 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.37e+00 bond pdb=" C ASP A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 1.335 1.348 -0.014 1.31e-02 5.83e+03 1.07e+00 bond pdb=" N GLU A1369 " pdb=" CA GLU A1369 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.72e-01 bond pdb=" N GLU A 329 " pdb=" CA GLU A 329 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.52e-01 ... (remaining 7290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 6959 1.50 - 3.01: 276 3.01 - 4.51: 40 4.51 - 6.02: 11 6.02 - 7.52: 5 Bond angle restraints: 7291 Sorted by residual: angle pdb=" N ILE A1684 " pdb=" CA ILE A1684 " pdb=" C ILE A1684 " ideal model delta sigma weight residual 113.20 108.21 4.99 9.60e-01 1.09e+00 2.71e+01 angle pdb=" N GLU A1947 " pdb=" CA GLU A1947 " pdb=" C GLU A1947 " ideal model delta sigma weight residual 110.91 116.95 -6.04 1.17e+00 7.31e-01 2.67e+01 angle pdb=" C ILE A 403 " pdb=" N GLU A 404 " pdb=" CA GLU A 404 " ideal model delta sigma weight residual 120.31 113.31 7.00 1.52e+00 4.33e-01 2.12e+01 angle pdb=" N ASP A2126 " pdb=" CA ASP A2126 " pdb=" C ASP A2126 " ideal model delta sigma weight residual 114.62 109.75 4.87 1.14e+00 7.69e-01 1.82e+01 angle pdb=" N ILE A1809 " pdb=" CA ILE A1809 " pdb=" C ILE A1809 " ideal model delta sigma weight residual 113.53 109.48 4.05 9.80e-01 1.04e+00 1.71e+01 ... (remaining 7286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.18: 1953 6.18 - 12.35: 414 12.35 - 18.53: 56 18.53 - 24.70: 5 24.70 - 30.88: 1 Dihedral angle restraints: 2429 sinusoidal: 0 harmonic: 2429 Sorted by residual: dihedral pdb=" CA GLU A1947 " pdb=" C GLU A1947 " pdb=" N TRP A1948 " pdb=" CA TRP A1948 " ideal model delta harmonic sigma weight residual 180.00 149.12 30.88 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA ILE A 813 " pdb=" C ILE A 813 " pdb=" N GLU A 814 " pdb=" CA GLU A 814 " ideal model delta harmonic sigma weight residual -180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU A1404 " pdb=" C LEU A1404 " pdb=" N THR A1405 " pdb=" CA THR A1405 " ideal model delta harmonic sigma weight residual -180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 2426 not shown) Chirality restraints: 0 Planarity restraints: 0 Histogram of nonbonded interaction distances: 2.57 - 3.04: 1925 3.04 - 3.50: 2617 3.50 - 3.97: 4896 3.97 - 4.43: 5866 4.43 - 4.90: 10075 Nonbonded interactions: 25379 Sorted by model distance: nonbonded pdb=" N ILE A1684 " pdb=" N ASP A1685 " model vdw 2.573 2.560 nonbonded pdb=" N ILE A1031 " pdb=" N ILE A1032 " model vdw 2.599 2.560 nonbonded pdb=" N ILE A1590 " pdb=" N LYS A1591 " model vdw 2.606 2.560 nonbonded pdb=" N GLY A1667 " pdb=" N ASP A1668 " model vdw 2.661 2.560 nonbonded pdb=" N VAL A1352 " pdb=" N ARG A1353 " model vdw 2.662 2.560 ... (remaining 25374 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.020 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7295 Z= 0.153 Angle : 0.742 7.522 7291 Z= 0.486 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.054 30.879 2429 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.09 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.17), residues: 2425 helix: 0.47 (0.21), residues: 597 sheet: -0.38 (0.30), residues: 308 loop : -1.40 (0.16), residues: 1520 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 7295) covalent geometry : angle 0.74161 ( 7291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.415 Fit side-chains TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0304 time to fit residues: 3.1734 Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.135756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.089546 restraints weight = 21099.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.083617 restraints weight = 22066.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.082884 restraints weight = 31613.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.082927 restraints weight = 28797.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.083012 restraints weight = 26306.991| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 7295 Z= 0.498 Angle : 1.106 9.512 7291 Z= 0.723 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.511 32.422 2429 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.01 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.16), residues: 2425 helix: -1.59 (0.21), residues: 490 sheet: -0.96 (0.28), residues: 330 loop : -1.95 (0.15), residues: 1605 Details of bonding type rmsd covalent geometry : bond 0.00654 ( 7295) covalent geometry : angle 1.10606 ( 7291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.368 Fit side-chains TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0310 time to fit residues: 3.2870 Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 239 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 187 optimal weight: 0.0980 chunk 178 optimal weight: 2.9990 chunk 164 optimal weight: 0.0770 chunk 170 optimal weight: 5.9990 chunk 107 optimal weight: 0.0170 chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.138898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.086670 restraints weight = 20692.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.085264 restraints weight = 22356.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.084785 restraints weight = 26110.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.084744 restraints weight = 26204.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.084733 restraints weight = 25505.477| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7295 Z= 0.148 Angle : 0.520 5.882 7291 Z= 0.327 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.343 18.097 2429 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.34 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.16), residues: 2425 helix: -0.77 (0.22), residues: 504 sheet: -0.84 (0.29), residues: 336 loop : -1.69 (0.15), residues: 1585 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 7295) covalent geometry : angle 0.51966 ( 7291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.337 Fit side-chains TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0281 time to fit residues: 3.0478 Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 242 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 100 optimal weight: 0.0970 chunk 208 optimal weight: 9.9990 chunk 39 optimal weight: 0.0970 chunk 101 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 overall best weight: 2.0382 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.133461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.082053 restraints weight = 21291.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.080655 restraints weight = 23368.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.080266 restraints weight = 24794.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.080014 restraints weight = 25629.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.079951 restraints weight = 25831.604| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.8399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 7295 Z= 0.287 Angle : 0.748 6.997 7291 Z= 0.482 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.729 24.806 2429 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 13.15 % Favored : 86.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.16), residues: 2425 helix: -1.51 (0.21), residues: 483 sheet: -0.76 (0.30), residues: 286 loop : -2.09 (0.14), residues: 1656 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7295) covalent geometry : angle 0.74781 ( 7291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.359 Fit side-chains TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0265 time to fit residues: 2.9268 Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 107 optimal weight: 0.0570 chunk 9 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 22 optimal weight: 0.0670 chunk 182 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 1.1640 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.134894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.085028 restraints weight = 21188.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.082960 restraints weight = 23109.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.082390 restraints weight = 25554.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.082254 restraints weight = 27067.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.082221 restraints weight = 26736.864| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.8457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7295 Z= 0.165 Angle : 0.504 5.365 7291 Z= 0.320 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.148 17.673 2429 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.32 % Favored : 90.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.16), residues: 2425 helix: -0.87 (0.22), residues: 501 sheet: -0.86 (0.30), residues: 312 loop : -2.03 (0.15), residues: 1612 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7295) covalent geometry : angle 0.50446 ( 7291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.455 Fit side-chains TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0284 time to fit residues: 3.1616 Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 51 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 180 optimal weight: 0.2980 chunk 148 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.126829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.076413 restraints weight = 21336.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.075282 restraints weight = 24083.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.074951 restraints weight = 25073.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.074779 restraints weight = 25856.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.074684 restraints weight = 26502.100| |-----------------------------------------------------------------------------| r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 1.0307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 7295 Z= 0.517 Angle : 1.091 8.166 7291 Z= 0.714 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.254 37.690 2429 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.54 % Allowed : 17.61 % Favored : 81.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.15), residues: 2425 helix: -2.56 (0.21), residues: 414 sheet: -1.51 (0.34), residues: 227 loop : -2.62 (0.14), residues: 1784 Details of bonding type rmsd covalent geometry : bond 0.00711 ( 7295) covalent geometry : angle 1.09074 ( 7291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.345 Fit side-chains TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0270 time to fit residues: 2.9555 Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 225 optimal weight: 8.9990 chunk 153 optimal weight: 0.0000 chunk 37 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 226 optimal weight: 0.9980 chunk 71 optimal weight: 0.0770 chunk 211 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.130773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.081038 restraints weight = 21168.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.080119 restraints weight = 23438.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.079842 restraints weight = 25900.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.079691 restraints weight = 26371.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.079659 restraints weight = 25856.669| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 1.0068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7295 Z= 0.194 Angle : 0.595 4.696 7291 Z= 0.376 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.815 22.983 2429 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.79 % Favored : 88.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.16), residues: 2425 helix: -1.93 (0.22), residues: 443 sheet: -1.20 (0.35), residues: 225 loop : -2.46 (0.14), residues: 1757 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7295) covalent geometry : angle 0.59473 ( 7291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.338 Fit side-chains TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0272 time to fit residues: 2.9801 Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 144 optimal weight: 0.0670 chunk 224 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 78 optimal weight: 0.0000 overall best weight: 0.7924 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.132103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.090639 restraints weight = 21185.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085453 restraints weight = 22505.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.085132 restraints weight = 26964.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.085282 restraints weight = 24869.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085380 restraints weight = 22644.674| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 1.0021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7295 Z= 0.111 Angle : 0.418 3.359 7291 Z= 0.262 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 3.615 17.113 2429 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.33 % Favored : 87.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.17), residues: 2425 helix: -1.05 (0.24), residues: 440 sheet: -0.97 (0.35), residues: 241 loop : -2.24 (0.15), residues: 1744 Details of bonding type rmsd covalent geometry : bond 0.00154 ( 7295) covalent geometry : angle 0.41764 ( 7291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.336 Fit side-chains TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0301 time to fit residues: 3.1313 Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 233 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 183 optimal weight: 0.0010 chunk 239 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 156 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 overall best weight: 2.4792 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.127720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.078603 restraints weight = 21025.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.077624 restraints weight = 22832.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.077038 restraints weight = 26708.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.076938 restraints weight = 26251.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.076926 restraints weight = 26694.761| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 1.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 7295 Z= 0.330 Angle : 0.785 11.057 7291 Z= 0.505 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.717 26.422 2429 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 18.85 % Favored : 80.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.29 (0.16), residues: 2425 helix: -1.87 (0.23), residues: 414 sheet: -1.51 (0.36), residues: 219 loop : -2.56 (0.14), residues: 1792 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 7295) covalent geometry : angle 0.78489 ( 7291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.341 Fit side-chains TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0295 time to fit residues: 3.2467 Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 234 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 204 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 46 optimal weight: 5.9990 chunk 182 optimal weight: 0.3980 chunk 187 optimal weight: 7.9990 chunk 86 optimal weight: 0.0020 chunk 107 optimal weight: 0.3980 overall best weight: 0.2988 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.132743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.090157 restraints weight = 21203.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.085178 restraints weight = 21884.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.084395 restraints weight = 29547.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.084034 restraints weight = 34232.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.084199 restraints weight = 27935.370| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 1.0485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.023 7295 Z= 0.059 Angle : 0.338 2.749 7291 Z= 0.209 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 3.019 15.892 2429 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.12 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.17), residues: 2425 helix: -0.45 (0.25), residues: 463 sheet: -0.99 (0.36), residues: 230 loop : -2.24 (0.15), residues: 1732 Details of bonding type rmsd covalent geometry : bond 0.00081 ( 7295) covalent geometry : angle 0.33810 ( 7291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4850 Ramachandran restraints generated. 2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.358 Fit side-chains TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0267 time to fit residues: 2.9612 Evaluate side-chains 47 residues out of total 2199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 76 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.127733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.078828 restraints weight = 21128.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.077808 restraints weight = 22723.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.076978 restraints weight = 27178.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.076939 restraints weight = 27132.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.076918 restraints weight = 27173.560| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 1.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 7295 Z= 0.290 Angle : 0.687 9.293 7291 Z= 0.444 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.047 23.225 2429 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 18.52 % Favored : 81.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.17), residues: 2425 helix: -1.33 (0.25), residues: 432 sheet: -1.23 (0.37), residues: 214 loop : -2.42 (0.14), residues: 1779 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7295) covalent geometry : angle 0.68726 ( 7291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.74 seconds wall clock time: 32 minutes 2.74 seconds (1922.74 seconds total)