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/6xtb_10618/12_2023/6xtb_10618.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtb_10618/12_2023/6xtb_10618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtb_10618/12_2023/6xtb_10618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtb_10618/12_2023/6xtb_10618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtb_10618/12_2023/6xtb_10618.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtb_10618/12_2023/6xtb_10618.pdb" } resolution = 4.3 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= 0.002 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: 3 Type Number sf(0) Gaussians C 691 2.51 5 N 235 2.21 5 O 235 1.98 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: 1161 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1161 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 212} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 750 Unresolved non-hydrogen angles: 966 Unresolved non-hydrogen dihedrals: 614 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 18, 'TRP:plan': 4, 'ASP:plan': 13, 'PHE:plan': 10, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 415 Time building chain proxies: 1.38, per 1000 atoms: 1.19 Number of scatterers: 1161 At special positions: 0 Unit cell: (57.78, 80.25, 70.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 235 8.00 N 235 7.00 C 691 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: 0.40 Conformation dependent library (CDL) restraints added in 491.4 milliseconds 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 442 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 3 sheets defined 11.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'E' and resid 119 through 134 removed outlier: 3.534A pdb=" N MET E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS E 128 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 253 removed outlier: 3.982A pdb=" N LYS E 248 " --> pdb=" O GLN E 244 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU E 249 " --> pdb=" O GLU E 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 57 through 58 removed outlier: 5.981A pdb=" N GLY E 48 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP E 32 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE E 106 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE E 97 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 95 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR E 96 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE E 79 " --> pdb=" O TYR E 96 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU E 98 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 160 through 167 removed outlier: 6.309A pdb=" N ILE E 182 " --> pdb=" O TYR E 161 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS E 163 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE E 180 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASN E 165 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY E 178 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE E 181 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL E 188 " --> pdb=" O PHE E 181 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR E 183 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ARG E 186 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL E 199 " --> pdb=" O TRP E 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 206 through 212 36 hydrogen bonds defined for protein. 105 hydrogen bond angles 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: 0.27 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 235 1.29 - 1.35: 232 1.35 - 1.41: 1 1.41 - 1.48: 234 1.48 - 1.54: 457 Bond restraints: 1159 Sorted by residual: bond pdb=" C ARG E 25 " pdb=" N PRO E 26 " ideal model delta sigma weight residual 1.333 1.359 -0.026 1.17e-02 7.31e+03 5.11e+00 bond pdb=" CA VAL E 240 " pdb=" CB VAL E 240 " ideal model delta sigma weight residual 1.544 1.521 0.023 1.25e-02 6.40e+03 3.52e+00 bond pdb=" CA VAL E 13 " pdb=" CB VAL E 13 " ideal model delta sigma weight residual 1.544 1.521 0.023 1.25e-02 6.40e+03 3.42e+00 bond pdb=" CA VAL E 71 " pdb=" CB VAL E 71 " ideal model delta sigma weight residual 1.548 1.522 0.027 1.49e-02 4.50e+03 3.27e+00 bond pdb=" CA ILE E 211 " pdb=" CB ILE E 211 " ideal model delta sigma weight residual 1.541 1.521 0.021 1.27e-02 6.20e+03 2.61e+00 ... (remaining 1154 not shown) Histogram of bond angle deviations from ideal: 105.85 - 110.30: 230 110.30 - 114.76: 446 114.76 - 119.22: 264 119.22 - 123.68: 629 123.68 - 128.13: 42 Bond angle restraints: 1611 Sorted by residual: angle pdb=" N PRO E 156 " pdb=" CA PRO E 156 " pdb=" CB PRO E 156 " ideal model delta sigma weight residual 103.33 110.46 -7.13 9.30e-01 1.16e+00 5.87e+01 angle pdb=" N PRO E 115 " pdb=" CA PRO E 115 " pdb=" CB PRO E 115 " ideal model delta sigma weight residual 101.88 109.35 -7.47 1.01e+00 9.80e-01 5.47e+01 angle pdb=" N PRO E 239 " pdb=" CA PRO E 239 " pdb=" CB PRO E 239 " ideal model delta sigma weight residual 103.25 110.99 -7.74 1.05e+00 9.07e-01 5.44e+01 angle pdb=" N PRO E 26 " pdb=" CA PRO E 26 " pdb=" CB PRO E 26 " ideal model delta sigma weight residual 103.36 109.66 -6.30 8.80e-01 1.29e+00 5.12e+01 angle pdb=" N PRO E 202 " pdb=" CA PRO E 202 " pdb=" CB PRO E 202 " ideal model delta sigma weight residual 102.85 110.70 -7.85 1.13e+00 7.83e-01 4.82e+01 ... (remaining 1606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.55: 550 5.55 - 11.11: 83 11.11 - 16.66: 33 16.66 - 22.21: 3 22.21 - 27.76: 6 Dihedral angle restraints: 675 sinusoidal: 0 harmonic: 675 Sorted by residual: dihedral pdb=" CA ILE E 57 " pdb=" C ILE E 57 " pdb=" N LEU E 58 " pdb=" CA LEU E 58 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA TYR E 96 " pdb=" C TYR E 96 " pdb=" N ILE E 97 " pdb=" CA ILE E 97 " ideal model delta harmonic sigma weight residual -180.00 -152.76 -27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LYS E 87 " pdb=" C LYS E 87 " pdb=" N LEU E 88 " pdb=" CA LEU E 88 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 152 0.059 - 0.119: 61 0.119 - 0.178: 2 0.178 - 0.237: 3 0.237 - 0.296: 3 Chirality restraints: 221 Sorted by residual: chirality pdb=" CA PRO E 115 " pdb=" N PRO E 115 " pdb=" C PRO E 115 " pdb=" CB PRO E 115 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA PRO E 118 " pdb=" N PRO E 118 " pdb=" C PRO E 118 " pdb=" CB PRO E 118 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA PRO E 26 " pdb=" N PRO E 26 " pdb=" C PRO E 26 " pdb=" CB PRO E 26 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 218 not shown) Planarity restraints: 233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 88 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C LEU E 88 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU E 88 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG E 89 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 41 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C LYS E 41 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS E 41 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY E 42 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 217 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C GLY E 217 " -0.024 2.00e-02 2.50e+03 pdb=" O GLY E 217 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU E 218 " 0.008 2.00e-02 2.50e+03 ... (remaining 230 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 429 2.88 - 3.38: 916 3.38 - 3.89: 1490 3.89 - 4.39: 1327 4.39 - 4.90: 2446 Nonbonded interactions: 6608 Sorted by model distance: nonbonded pdb=" N ARG E 49 " pdb=" O HIS E 60 " model vdw 2.369 2.520 nonbonded pdb=" N THR E 92 " pdb=" N GLU E 93 " model vdw 2.524 2.560 nonbonded pdb=" O SER E 36 " pdb=" N THR E 111 " model vdw 2.531 2.520 nonbonded pdb=" N THR E 83 " pdb=" O THR E 83 " model vdw 2.599 2.496 nonbonded pdb=" N ILE E 37 " pdb=" O GLY E 48 " model vdw 2.605 2.520 ... (remaining 6603 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: 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: 4.300 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.610 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4468 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 : 0.006 0.027 1159 Z= 0.460 Angle : 1.171 7.847 1611 Z= 0.835 Chirality : 0.066 0.296 221 Planarity : 0.004 0.020 233 Dihedral : 8.676 27.764 233 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.58 % Favored : 84.42 % 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: -4.66 (0.42), residues: 231 helix: -4.08 (0.49), residues: 32 sheet: -3.25 (0.72), residues: 33 loop : -3.08 (0.39), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.143 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0372 time to fit residues: 0.3677 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 14 optimal weight: 40.0000 overall best weight: 5.0786 ------------------------------------------------------------------------------- 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: 0.5104 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 1159 Z= 0.198 Angle : 0.612 4.111 1611 Z= 0.373 Chirality : 0.049 0.141 221 Planarity : 0.003 0.011 233 Dihedral : 5.840 15.576 233 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % 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: -4.79 (0.42), residues: 231 helix: -3.80 (0.52), residues: 33 sheet: -2.79 (0.64), residues: 58 loop : -3.33 (0.38), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.140 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0151 time to fit residues: 0.2887 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.137 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 5 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.8639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1159 Z= 0.199 Angle : 0.616 4.806 1611 Z= 0.372 Chirality : 0.049 0.136 221 Planarity : 0.003 0.008 233 Dihedral : 6.084 16.767 233 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % 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: -4.51 (0.46), residues: 231 helix: -3.50 (0.57), residues: 33 sheet: -2.47 (0.76), residues: 47 loop : -3.24 (0.43), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.141 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0164 time to fit residues: 0.2980 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 20 optimal weight: 40.0000 chunk 22 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 40.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- 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: 0.5529 moved from start: 1.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1159 Z= 0.288 Angle : 0.829 7.141 1611 Z= 0.491 Chirality : 0.050 0.129 221 Planarity : 0.005 0.014 233 Dihedral : 7.784 25.803 233 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.43 % Allowed : 19.91 % Favored : 79.65 % 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: -5.07 (0.47), residues: 231 helix: -3.21 (0.73), residues: 32 sheet: -2.38 (0.71), residues: 57 loop : -4.07 (0.41), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.137 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0155 time to fit residues: 0.3020 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 40.0000 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 40.0000 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 22 optimal weight: 0.3980 chunk 18 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 overall best weight: 6.8790 ------------------------------------------------------------------------------- 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: 0.5546 moved from start: 1.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1159 Z= 0.217 Angle : 0.675 6.133 1611 Z= 0.399 Chirality : 0.048 0.131 221 Planarity : 0.003 0.013 233 Dihedral : 6.792 24.399 233 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.58 % Favored : 84.42 % 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: -5.03 (0.48), residues: 231 helix: -3.21 (0.72), residues: 32 sheet: -2.57 (0.66), residues: 62 loop : -3.94 (0.44), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0163 time to fit residues: 0.2924 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 40.0000 chunk 21 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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: 0.5649 moved from start: 1.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1159 Z= 0.255 Angle : 0.790 6.786 1611 Z= 0.467 Chirality : 0.049 0.126 221 Planarity : 0.004 0.014 233 Dihedral : 7.934 24.120 233 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.51 % Favored : 77.49 % 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: -5.12 (0.48), residues: 231 helix: -2.92 (0.78), residues: 32 sheet: -2.34 (0.74), residues: 56 loop : -4.22 (0.42), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.144 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0159 time to fit residues: 0.2989 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 40.0000 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 2 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 50.0000 chunk 21 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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: 0.5661 moved from start: 1.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1159 Z= 0.245 Angle : 0.741 6.688 1611 Z= 0.441 Chirality : 0.049 0.126 221 Planarity : 0.004 0.011 233 Dihedral : 7.775 25.874 233 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.05 % Favored : 80.95 % 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: -5.28 (0.46), residues: 231 helix: -2.73 (0.80), residues: 31 sheet: -3.43 (0.74), residues: 44 loop : -3.97 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.145 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0158 time to fit residues: 0.2869 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.137 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 19 optimal weight: 40.0000 chunk 20 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 40.0000 chunk 15 optimal weight: 8.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- 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: 0.5719 moved from start: 1.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1159 Z= 0.255 Angle : 0.786 7.651 1611 Z= 0.468 Chirality : 0.049 0.126 221 Planarity : 0.004 0.014 233 Dihedral : 8.220 24.717 233 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.81 % Favored : 76.19 % 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: -5.35 (0.47), residues: 231 helix: -2.79 (0.81), residues: 31 sheet: -2.86 (0.88), residues: 37 loop : -4.22 (0.40), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.147 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0171 time to fit residues: 0.3134 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 7 optimal weight: 0.0980 overall best weight: 4.6188 ------------------------------------------------------------------------------- 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: 0.5647 moved from start: 1.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1159 Z= 0.155 Angle : 0.625 6.773 1611 Z= 0.370 Chirality : 0.048 0.124 221 Planarity : 0.003 0.010 233 Dihedral : 6.886 24.593 233 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.75 % Favored : 82.25 % 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: -5.28 (0.48), residues: 231 helix: -2.63 (0.82), residues: 31 sheet: -3.30 (0.68), residues: 57 loop : -4.01 (0.43), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0155 time to fit residues: 0.2844 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.136 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 1 optimal weight: 0.0060 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 12 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 overall best weight: 8.6006 ------------------------------------------------------------------------------- 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: 0.5735 moved from start: 1.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1159 Z= 0.256 Angle : 0.769 7.633 1611 Z= 0.459 Chirality : 0.049 0.126 221 Planarity : 0.004 0.012 233 Dihedral : 8.175 24.818 233 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.11 % Favored : 74.89 % 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: -5.53 (0.47), residues: 231 helix: -2.86 (0.77), residues: 32 sheet: -3.04 (0.75), residues: 50 loop : -4.38 (0.41), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.160 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0148 time to fit residues: 0.2648 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 overall best weight: 10.0090 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.081661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.070785 restraints weight = 8856.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.071507 restraints weight = 7088.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.071888 restraints weight = 6086.493| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 1.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1159 Z= 0.292 Angle : 0.836 8.000 1611 Z= 0.502 Chirality : 0.050 0.127 221 Planarity : 0.004 0.013 233 Dihedral : 9.133 27.732 233 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.11 % Favored : 74.89 % 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: -5.72 (0.47), residues: 231 helix: -3.52 (0.70), residues: 31 sheet: -3.16 (0.76), residues: 50 loop : -4.38 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP E 8 PHE 0.000 0.000 PHE E 15 TYR 0.000 0.000 TYR E 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 581.64 seconds wall clock time: 14 minutes 3.36 seconds (843.36 seconds total)