Starting phenix.real_space_refine on Wed Mar 12 01:56:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n9q_24259/03_2025/7n9q_24259.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n9q_24259/03_2025/7n9q_24259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n9q_24259/03_2025/7n9q_24259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n9q_24259/03_2025/7n9q_24259.map" model { file = "/net/cci-nas-00/data/ceres_data/7n9q_24259/03_2025/7n9q_24259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n9q_24259/03_2025/7n9q_24259.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 2 Type Number sf(0) Gaussians C 4630 2.51 5 N 2315 2.21 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6945 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2315, 6945 Classifications: {'peptide': 2315} Incomplete info: {'n_c_alpha_c_only': 2315} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 2264} Chain breaks: 2 Unresolved chain link angles: 2364 Unresolved non-hydrogen bonds: 12079 Unresolved non-hydrogen angles: 16444 Unresolved non-hydrogen dihedrals: 6273 Unresolved non-hydrogen chiralities: 2840 Planarities with less than four sites: {'GLN:plan1': 58, 'HIS:plan': 23, 'TYR:plan': 134, 'ASN:plan1': 192, 'TRP:plan': 16, 'ASP:plan': 180, 'PHE:plan': 132, 'GLU:plan': 205, 'ARG:plan': 48} Unresolved non-hydrogen planarities: 5074 Time building chain proxies: 6.48, per 1000 atoms: 0.93 Number of scatterers: 6945 At special positions: 0 Unit cell: (134.703, 146.37, 256.677, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 2 Type Number sf(0) N 2315 7.00 C 4630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 1.8 seconds 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.32 - 1.36: 2312 1.36 - 1.41: 0 1.41 - 1.45: 123 1.45 - 1.50: 2192 1.50 - 1.54: 2315 Bond restraints: 6942 Sorted by residual: bond pdb=" CA VAL A1094 " pdb=" C VAL A1094 " ideal model delta sigma weight residual 1.525 1.540 -0.015 8.80e-03 1.29e+04 2.76e+00 bond pdb=" N ASP A 442 " pdb=" CA ASP A 442 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.54e+00 bond pdb=" CA ASP A1500 " pdb=" C ASP A1500 " ideal model delta sigma weight residual 1.523 1.532 -0.009 8.40e-03 1.42e+04 1.04e+00 bond pdb=" N ASN A1839 " pdb=" CA ASN A1839 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.99e-01 bond pdb=" N SER A1242 " pdb=" CA SER A1242 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.78e-01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 6754 2.29 - 4.57: 152 4.57 - 6.86: 28 6.86 - 9.15: 2 9.15 - 11.43: 3 Bond angle restraints: 6939 Sorted by residual: angle pdb=" C ALA A 441 " pdb=" N ASP A 442 " pdb=" CA ASP A 442 " ideal model delta sigma weight residual 121.54 132.97 -11.43 1.91e+00 2.74e-01 3.58e+01 angle pdb=" C PHE A2069 " pdb=" N ASP A2070 " pdb=" CA ASP A2070 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C GLN A 193 " pdb=" N ARG A 194 " pdb=" CA ARG A 194 " ideal model delta sigma weight residual 121.58 112.24 9.34 1.95e+00 2.63e-01 2.29e+01 angle pdb=" N TYR A2223 " pdb=" CA TYR A2223 " pdb=" C TYR A2223 " ideal model delta sigma weight residual 114.75 109.14 5.61 1.26e+00 6.30e-01 1.98e+01 angle pdb=" C LYS A 76 " pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta sigma weight residual 120.31 114.02 6.29 1.52e+00 4.33e-01 1.71e+01 ... (remaining 6934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.68: 1687 5.68 - 11.36: 505 11.36 - 17.04: 98 17.04 - 22.71: 19 22.71 - 28.39: 3 Dihedral angle restraints: 2312 sinusoidal: 0 harmonic: 2312 Sorted by residual: dihedral pdb=" CA TYR A2213 " pdb=" C TYR A2213 " pdb=" N ASP A2214 " pdb=" CA ASP A2214 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA THR A1234 " pdb=" C THR A1234 " pdb=" N GLY A1235 " pdb=" CA GLY A1235 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA GLU A1212 " pdb=" C GLU A1212 " pdb=" N LEU A1213 " pdb=" CA LEU A1213 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 2309 not shown) Chirality restraints: 0 Planarity restraints: 0 Histogram of nonbonded interaction distances: 2.60 - 3.06: 1995 3.06 - 3.52: 2446 3.52 - 3.98: 4853 3.98 - 4.44: 6241 4.44 - 4.90: 9761 Nonbonded interactions: 25296 Sorted by model distance: nonbonded pdb=" N ASP A 442 " pdb=" N ASN A 443 " model vdw 2.600 2.560 nonbonded pdb=" N ASP A1812 " pdb=" N LEU A1813 " model vdw 2.603 2.560 nonbonded pdb=" N ILE A1809 " pdb=" N GLY A1810 " model vdw 2.606 2.560 nonbonded pdb=" N ASP A2214 " pdb=" N MET A2215 " model vdw 2.618 2.560 nonbonded pdb=" N GLY A1088 " pdb=" N PHE A1089 " model vdw 2.627 2.560 ... (remaining 25291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.700 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 6942 Z= 0.171 Angle : 0.883 11.435 6939 Z= 0.561 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.650 28.393 2312 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.78 % Allowed : 8.92 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2309 helix: 0.26 (0.21), residues: 569 sheet: -0.42 (0.26), residues: 374 loop : -1.90 (0.16), residues: 1366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.894 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0595 time to fit residues: 6.4184 Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 6.9990 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 93 optimal weight: 0.0020 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 0.0570 chunk 110 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 overall best weight: 0.8708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.127630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.070780 restraints weight = 15854.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.069998 restraints weight = 18598.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.069998 restraints weight = 20238.966| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6942 Z= 0.126 Angle : 0.520 5.275 6939 Z= 0.326 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.362 22.589 2312 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.49 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.17), residues: 2309 helix: 1.51 (0.22), residues: 553 sheet: -0.54 (0.25), residues: 410 loop : -1.82 (0.16), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.881 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0610 time to fit residues: 6.7430 Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 125 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.049232 restraints weight = 15574.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.049232 restraints weight = 17836.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.049232 restraints weight = 17836.095| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 1.0414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 6942 Z= 0.563 Angle : 1.539 17.486 6939 Z= 0.968 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 9.938 36.057 2312 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 34.31 Ramachandran Plot: Outliers : 1.43 % Allowed : 15.89 % Favored : 82.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.15), residues: 2309 helix: -2.70 (0.24), residues: 299 sheet: -1.49 (0.32), residues: 243 loop : -2.60 (0.13), residues: 1767 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.932 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0607 time to fit residues: 6.7710 Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 171 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 86 optimal weight: 0.0070 chunk 170 optimal weight: 7.9990 chunk 6 optimal weight: 0.0770 chunk 193 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 2.8162 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.102978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.051364 restraints weight = 15802.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.050134 restraints weight = 18351.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.050132 restraints weight = 20914.796| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 1.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6942 Z= 0.315 Angle : 1.012 21.672 6939 Z= 0.624 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.515 39.071 2312 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.87 % Allowed : 15.59 % Favored : 83.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.15), residues: 2309 helix: -2.38 (0.24), residues: 338 sheet: -1.82 (0.30), residues: 272 loop : -2.78 (0.14), residues: 1699 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.882 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0550 time to fit residues: 6.1282 Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 13 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 206 optimal weight: 0.0030 overall best weight: 4.1998 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.096642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.047498 restraints weight = 16403.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.046487 restraints weight = 18714.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.046487 restraints weight = 21161.591| |-----------------------------------------------------------------------------| r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 1.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 6942 Z= 0.468 Angle : 1.312 25.388 6939 Z= 0.816 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.966 44.788 2312 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 38.21 Ramachandran Plot: Outliers : 0.87 % Allowed : 22.78 % Favored : 76.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.15), residues: 2309 helix: -3.20 (0.23), residues: 293 sheet: -1.87 (0.33), residues: 234 loop : -3.17 (0.13), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.040 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0593 time to fit residues: 6.7342 Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 153 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 229 optimal weight: 30.0000 chunk 165 optimal weight: 0.4980 chunk 222 optimal weight: 5.9990 chunk 197 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 216 optimal weight: 0.0770 chunk 119 optimal weight: 8.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.107688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.071346 restraints weight = 29275.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.067429 restraints weight = 33107.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.066356 restraints weight = 44621.949| |-----------------------------------------------------------------------------| r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 1.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6942 Z= 0.134 Angle : 0.646 19.653 6939 Z= 0.385 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 5.614 24.647 2312 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.78 % Allowed : 12.17 % Favored : 87.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.16), residues: 2309 helix: -2.15 (0.25), residues: 339 sheet: -1.50 (0.33), residues: 244 loop : -3.02 (0.13), residues: 1726 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.306 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1034 time to fit residues: 11.0114 Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 174 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 199 optimal weight: 0.0770 chunk 142 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.095142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.047874 restraints weight = 17143.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.046901 restraints weight = 19876.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.046900 restraints weight = 22397.058| |-----------------------------------------------------------------------------| r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 1.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 6942 Z= 0.433 Angle : 1.211 22.158 6939 Z= 0.760 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.445 37.979 2312 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 36.95 Ramachandran Plot: Outliers : 0.91 % Allowed : 25.68 % Favored : 73.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.15), residues: 2309 helix: -2.96 (0.25), residues: 268 sheet: -2.02 (0.34), residues: 236 loop : -3.32 (0.13), residues: 1805 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.986 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0643 time to fit residues: 7.0348 Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 56 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 184 optimal weight: 0.4980 chunk 157 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.098480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.049724 restraints weight = 16374.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.048658 restraints weight = 18851.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.048658 restraints weight = 21328.089| |-----------------------------------------------------------------------------| r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 1.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6942 Z= 0.241 Angle : 0.835 19.616 6939 Z= 0.517 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.801 27.992 2312 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.82 % Allowed : 18.28 % Favored : 80.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.15), residues: 2309 helix: -2.82 (0.25), residues: 316 sheet: -1.93 (0.34), residues: 243 loop : -3.23 (0.13), residues: 1750 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.910 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0579 time to fit residues: 6.3695 Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 85 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 0.0270 chunk 144 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 140 optimal weight: 0.0170 chunk 12 optimal weight: 8.9990 overall best weight: 2.8082 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.095915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.048080 restraints weight = 17427.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.047166 restraints weight = 20018.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.047165 restraints weight = 22327.836| |-----------------------------------------------------------------------------| r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 1.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6942 Z= 0.317 Angle : 0.949 19.594 6939 Z= 0.600 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.311 30.941 2312 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.82 % Allowed : 25.81 % Favored : 73.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.15), residues: 2309 helix: -2.77 (0.26), residues: 278 sheet: -2.08 (0.34), residues: 249 loop : -3.38 (0.13), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.972 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0653 time to fit residues: 7.2314 Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 218 optimal weight: 30.0000 chunk 140 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 0.0060 chunk 17 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 212 optimal weight: 0.0370 chunk 73 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.8080 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.097948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.049404 restraints weight = 17345.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.048477 restraints weight = 19954.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.048476 restraints weight = 22169.909| |-----------------------------------------------------------------------------| r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 1.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6942 Z= 0.214 Angle : 0.752 19.232 6939 Z= 0.468 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.292 26.805 2312 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.78 % Allowed : 19.66 % Favored : 79.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.16), residues: 2309 helix: -2.53 (0.26), residues: 298 sheet: -2.07 (0.34), residues: 247 loop : -3.29 (0.13), residues: 1764 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.921 Fit side-chains TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0603 time to fit residues: 6.5928 Evaluate side-chains 44 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 121 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 229 optimal weight: 50.0000 chunk 141 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.090401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.044385 restraints weight = 18003.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.043466 restraints weight = 20312.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.043455 restraints weight = 22786.697| |-----------------------------------------------------------------------------| r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 1.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 6942 Z= 0.600 Angle : 1.494 22.032 6939 Z= 0.950 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 9.552 56.430 2312 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 53.41 Ramachandran Plot: Outliers : 1.52 % Allowed : 30.58 % Favored : 67.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.15), residues: 2309 helix: -3.50 (0.24), residues: 244 sheet: -2.45 (0.40), residues: 185 loop : -3.73 (0.12), residues: 1880 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2752.78 seconds wall clock time: 47 minutes 42.88 seconds (2862.88 seconds total)