Starting phenix.real_space_refine on Thu Dec 7 15:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og3_20051/12_2023/6og3_20051.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og3_20051/12_2023/6og3_20051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og3_20051/12_2023/6og3_20051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og3_20051/12_2023/6og3_20051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og3_20051/12_2023/6og3_20051.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og3_20051/12_2023/6og3_20051.pdb" } resolution = 4.1 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= 0.000 sd= 0.001 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 810 2.51 5 N 405 2.21 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 1215 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 396 Classifications: {'peptide': 132} Incomplete info: {'n_c_alpha_c_only': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved chain link angles: 135 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 8, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 210 Chain: "C" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 396 Classifications: {'peptide': 132} Incomplete info: {'n_c_alpha_c_only': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved chain link angles: 135 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 8, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 210 Chain: "A" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 396 Classifications: {'peptide': 132} Incomplete info: {'n_c_alpha_c_only': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved chain link angles: 135 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 8, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 210 Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 27 Classifications: {'peptide': 9} Incomplete info: {'n_c_alpha_c_only': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 1.49, per 1000 atoms: 1.23 Number of scatterers: 1215 At special positions: 0 Unit cell: (54.696, 80.496, 75.336, 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 405 7.00 C 810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 372.4 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'E' and resid 7 through 24 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 7 through 24' Processing helix chain 'E' and resid 30 through 40 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 30 through 40' Processing helix chain 'E' and resid 45 through 54 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 45 through 54' Processing helix chain 'E' and resid 56 through 69 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 56 through 69' Processing helix chain 'E' and resid 84 through 102 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 84 through 102' Processing helix chain 'E' and resid 107 through 117 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 107 through 117' Processing helix chain 'E' and resid 119 through 129 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 119 through 129' Processing helix chain 'E' and resid 132 through 142 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 132 through 142' Processing helix chain 'C' and resid 7 through 24 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 7 through 24' Processing helix chain 'C' and resid 30 through 40 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 30 through 40' Processing helix chain 'C' and resid 45 through 54 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 45 through 54' Processing helix chain 'C' and resid 56 through 69 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 56 through 69' Processing helix chain 'C' and resid 84 through 102 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 84 through 102' Processing helix chain 'C' and resid 107 through 117 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 107 through 117' Processing helix chain 'C' and resid 119 through 129 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 119 through 129' Processing helix chain 'C' and resid 132 through 142 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 132 through 142' Processing helix chain 'A' and resid 7 through 24 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 7 through 24' Processing helix chain 'A' and resid 30 through 40 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 30 through 40' Processing helix chain 'A' and resid 45 through 54 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 45 through 54' Processing helix chain 'A' and resid 56 through 69 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 56 through 69' Processing helix chain 'A' and resid 84 through 102 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 84 through 102' Processing helix chain 'A' and resid 107 through 117 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 107 through 117' Processing helix chain 'A' and resid 119 through 129 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 119 through 129' Processing helix chain 'A' and resid 132 through 142 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 132 through 142' 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: 0.07 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.32 - 1.37: 398 1.37 - 1.41: 0 1.41 - 1.45: 19 1.45 - 1.49: 386 1.49 - 1.54: 405 Bond restraints: 1208 Sorted by residual: bond pdb=" N ASP E 4 " pdb=" CA ASP E 4 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.61e+00 bond pdb=" N ASP C 4 " pdb=" CA ASP C 4 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.40e+00 bond pdb=" N ASP A 4 " pdb=" CA ASP A 4 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.29e+00 bond pdb=" CA PRO A 31 " pdb=" C PRO A 31 " ideal model delta sigma weight residual 1.516 1.536 -0.020 1.72e-02 3.38e+03 1.33e+00 bond pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta sigma weight residual 1.456 1.471 -0.015 1.33e-02 5.65e+03 1.29e+00 ... (remaining 1203 not shown) Histogram of bond angle deviations from ideal: 101.50 - 105.93: 3 105.93 - 110.36: 163 110.36 - 114.79: 228 114.79 - 119.22: 421 119.22 - 123.64: 386 Bond angle restraints: 1201 Sorted by residual: angle pdb=" N VAL C 46 " pdb=" CA VAL C 46 " pdb=" C VAL C 46 " ideal model delta sigma weight residual 110.42 117.09 -6.67 9.60e-01 1.09e+00 4.83e+01 angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 110.42 117.08 -6.66 9.60e-01 1.09e+00 4.82e+01 angle pdb=" N VAL A 46 " pdb=" CA VAL A 46 " pdb=" C VAL A 46 " ideal model delta sigma weight residual 110.42 117.07 -6.65 9.60e-01 1.09e+00 4.81e+01 angle pdb=" N THR E 121 " pdb=" CA THR E 121 " pdb=" C THR E 121 " ideal model delta sigma weight residual 111.07 116.67 -5.60 1.07e+00 8.73e-01 2.74e+01 angle pdb=" N THR A 121 " pdb=" CA THR A 121 " pdb=" C THR A 121 " ideal model delta sigma weight residual 111.07 116.61 -5.54 1.07e+00 8.73e-01 2.68e+01 ... (remaining 1196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 0.84: 275 0.84 - 1.69: 96 1.69 - 2.53: 20 2.53 - 3.37: 3 3.37 - 4.22: 4 Dihedral angle restraints: 398 sinusoidal: 0 harmonic: 398 Sorted by residual: dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N MET A 35 " pdb=" CA MET A 35 " ideal model delta harmonic sigma weight residual 180.00 175.78 4.22 0 5.00e+00 4.00e-02 7.11e-01 dihedral pdb=" CA PHE E 28 " pdb=" C PHE E 28 " pdb=" N ILE E 29 " pdb=" CA ILE E 29 " ideal model delta harmonic sigma weight residual 180.00 176.36 3.64 0 5.00e+00 4.00e-02 5.31e-01 dihedral pdb=" CA PHE C 28 " pdb=" C PHE C 28 " pdb=" N ILE C 29 " pdb=" CA ILE C 29 " ideal model delta harmonic sigma weight residual 180.00 176.47 3.53 0 5.00e+00 4.00e-02 4.97e-01 ... (remaining 395 not shown) Chirality restraints: 0 Planarity restraints: 0 Histogram of nonbonded interaction distances: 2.54 - 3.01: 471 3.01 - 3.48: 547 3.48 - 3.95: 768 3.95 - 4.43: 1587 4.43 - 4.90: 2121 Nonbonded interactions: 5494 Sorted by model distance: nonbonded pdb=" N ARG E 5 " pdb=" N LEU E 6 " model vdw 2.539 2.560 nonbonded pdb=" N ARG A 5 " pdb=" N LEU A 6 " model vdw 2.539 2.560 nonbonded pdb=" N ARG C 5 " pdb=" N LEU C 6 " model vdw 2.541 2.560 nonbonded pdb=" N ALA C 53 " pdb=" N GLY C 54 " model vdw 2.629 2.560 nonbonded pdb=" N ALA E 53 " pdb=" N GLY E 54 " model vdw 2.630 2.560 ... (remaining 5489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } 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: 1.110 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: 3.300 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4858 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 : 0.005 0.031 1208 Z= 0.393 Angle : 1.530 7.041 1201 Z= 1.235 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 0.934 4.216 398 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.78 % Allowed : 0.00 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.36), residues: 384 helix: 0.09 (0.24), residues: 318 sheet: None (None), residues: 0 loop : 1.54 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.173 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0347 time to fit residues: 0.4195 Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 0.0670 chunk 16 optimal weight: 0.0020 chunk 10 optimal weight: 0.0270 chunk 19 optimal weight: 0.2980 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 0.0980 chunk 18 optimal weight: 0.0570 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 0.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4850 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.000 0.002 1208 Z= 0.020 Angle : 0.107 0.428 1201 Z= 0.081 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 1.583 3.560 398 Min Nonbonded Distance : 2.698 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.84 (0.43), residues: 384 helix: 2.61 (0.29), residues: 318 sheet: None (None), residues: 0 loop : 2.38 (0.74), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.181 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0135 time to fit residues: 0.3513 Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.196 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0070 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 0.0470 chunk 28 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 overall best weight: 3.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.9812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 1208 Z= 0.243 Angle : 0.598 2.537 1201 Z= 0.463 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.055 17.562 398 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.95 (0.37), residues: 384 helix: 1.53 (0.33), residues: 210 sheet: None (None), residues: 0 loop : 1.22 (0.39), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.179 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0150 time to fit residues: 0.3487 Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.0070 chunk 31 optimal weight: 0.2980 chunk 21 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 overall best weight: 2.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 1.0455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.006 1208 Z= 0.149 Angle : 0.400 2.084 1201 Z= 0.315 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 4.695 15.735 398 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.40), residues: 384 helix: 1.14 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 1.55 (0.46), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.154 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0137 time to fit residues: 0.3320 Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.176 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 0.0370 chunk 22 optimal weight: 20.0000 overall best weight: 14.0074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 1.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.030 1208 Z= 0.702 Angle : 1.292 5.646 1201 Z= 0.990 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 10.078 25.312 398 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 65.53 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.29 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.40), residues: 384 helix: -2.50 (0.31), residues: 180 sheet: None (None), residues: 0 loop : -0.18 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.173 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0183 time to fit residues: 0.3634 Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.167 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 36 optimal weight: 0.0870 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 overall best weight: 7.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 1.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 1208 Z= 0.418 Angle : 0.852 3.967 1201 Z= 0.664 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.221 22.245 398 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 42.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.41), residues: 384 helix: -2.28 (0.34), residues: 180 sheet: None (None), residues: 0 loop : -0.33 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.179 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0134 time to fit residues: 0.3542 Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 0.0870 chunk 11 optimal weight: 0.0040 chunk 7 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 4.0176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 1.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.010 1208 Z= 0.230 Angle : 0.561 2.873 1201 Z= 0.449 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.725 17.648 398 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.51 (0.42), residues: 384 helix: -1.64 (0.37), residues: 183 sheet: None (None), residues: 0 loop : -0.18 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.170 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0129 time to fit residues: 0.3410 Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 20.0000 chunk 29 optimal weight: 0.1980 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 35 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 overall best weight: 5.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 1.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.012 1208 Z= 0.280 Angle : 0.633 3.146 1201 Z= 0.504 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.103 17.925 398 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 38.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.43), residues: 384 helix: -1.57 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -0.08 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.177 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0133 time to fit residues: 0.3528 Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 0.0670 chunk 37 optimal weight: 10.0000 chunk 22 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 40.0000 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 overall best weight: 7.0128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 1.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.015 1208 Z= 0.373 Angle : 0.784 3.841 1201 Z= 0.617 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.880 19.949 398 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 45.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.42), residues: 384 helix: -1.94 (0.40), residues: 148 sheet: None (None), residues: 0 loop : -0.23 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.177 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0141 time to fit residues: 0.3607 Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.183 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 1.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.014 1208 Z= 0.327 Angle : 0.710 3.524 1201 Z= 0.563 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.501 18.652 398 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 42.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.47 (0.42), residues: 384 helix: -1.99 (0.40), residues: 150 sheet: None (None), residues: 0 loop : -0.14 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.175 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0137 time to fit residues: 0.3626 Evaluate side-chains 3 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.184 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 20 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 overall best weight: 7.2190 ------------------------------------------------------------------------------- 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 = 0.2503 r_free = 0.2503 target = 0.031760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2239 r_free = 0.2239 target = 0.023586 restraints weight = 12993.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.023528 restraints weight = 12791.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2229 r_free = 0.2229 target = 0.023554 restraints weight = 14034.623| |-----------------------------------------------------------------------------| r_work (final): 0.2204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 1.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.016 1208 Z= 0.381 Angle : 0.791 3.950 1201 Z= 0.623 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.007 20.633 398 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 51.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.64 (0.42), residues: 384 helix: -1.99 (0.41), residues: 142 sheet: None (None), residues: 0 loop : -0.42 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 569.72 seconds wall clock time: 10 minutes 56.11 seconds (656.11 seconds total)