Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtb_10618/09_2024/6xtb_10618.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtb_10618/09_2024/6xtb_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_10618/09_2024/6xtb_10618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtb_10618/09_2024/6xtb_10618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtb_10618/09_2024/6xtb_10618.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xtb_10618/09_2024/6xtb_10618.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 1.40, per 1000 atoms: 1.21 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 214.5 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: 0.25 Time building geometry restraints manager: 0.76 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: 0.00 - 1.57: 1417 1.57 - 3.14: 159 3.14 - 4.71: 23 4.71 - 6.28: 6 6.28 - 7.85: 6 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 3.120 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 3.120 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 3.120 ... (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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.120 Find NCS groups from input model: 0.020 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 12.900 ------------------------------------------------------------------------------- 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 : 0.142 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0368 time to fit residues: 0.3635 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 0.0050 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 14 optimal weight: 40.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- 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: 0.5158 moved from start: 0.5494 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= 0.203 Angle : 0.618 4.520 1611 Z= 0.376 Chirality : 0.049 0.135 221 Planarity : 0.003 0.011 233 Dihedral : 6.051 15.474 233 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.61 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: -4.84 (0.42), residues: 231 helix: -3.96 (0.47), residues: 33 sheet: -2.79 (0.66), residues: 56 loop : -3.35 (0.38), 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 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 : 0.139 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0152 time to fit residues: 0.2954 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 ------------------------------------------------------------------------------- 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: 20.0000 chunk 20 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 40.0000 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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: 0.5314 moved from start: 0.7336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 1159 Z= 0.150 Angle : 0.494 3.509 1611 Z= 0.301 Chirality : 0.048 0.130 221 Planarity : 0.002 0.006 233 Dihedral : 4.773 15.052 233 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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: -4.39 (0.46), residues: 231 helix: -3.43 (0.57), residues: 33 sheet: -2.41 (0.67), residues: 60 loop : -3.14 (0.43), residues: 138 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 : 0.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0158 time to fit residues: 0.2954 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 40.0000 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 40.0000 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- 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: 0.5548 moved from start: 1.0641 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= 0.276 Angle : 0.795 8.177 1611 Z= 0.471 Chirality : 0.050 0.133 221 Planarity : 0.004 0.014 233 Dihedral : 7.540 26.169 233 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % 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: -4.80 (0.49), residues: 231 helix: -3.45 (0.68), residues: 33 sheet: -2.10 (0.74), residues: 56 loop : -3.80 (0.44), 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: 0.0153 time to fit residues: 0.2848 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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: 40.0000 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 40.0000 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 40.0000 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 22 optimal weight: 0.2980 chunk 18 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 overall best weight: 6.4588 ------------------------------------------------------------------------------- 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: 0.5531 moved from start: 1.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1159 Z= 0.204 Angle : 0.639 5.647 1611 Z= 0.377 Chirality : 0.048 0.126 221 Planarity : 0.003 0.010 233 Dihedral : 6.422 22.528 233 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % 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: -4.86 (0.51), residues: 231 helix: -3.33 (0.66), residues: 33 sheet: -2.73 (0.62), residues: 71 loop : -3.59 (0.51), residues: 127 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 : 0.131 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0153 time to fit residues: 0.2836 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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: 20.0000 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 40.0000 chunk 21 optimal weight: 50.0000 chunk 2 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 overall best weight: 13.9994 ------------------------------------------------------------------------------- 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: 1.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 1159 Z= 0.412 Angle : 1.021 7.372 1611 Z= 0.611 Chirality : 0.053 0.140 221 Planarity : 0.006 0.022 233 Dihedral : 9.712 29.747 233 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.97 % Favored : 74.03 % 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: -5.74 (0.44), residues: 231 helix: -3.24 (0.73), residues: 31 sheet: -3.40 (0.73), residues: 47 loop : -4.37 (0.38), residues: 153 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 : 0.124 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0160 time to fit residues: 0.2881 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 ------------------------------------------------------------------------------- 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: 20.0000 chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 2 optimal weight: 0.0470 chunk 17 optimal weight: 30.0000 chunk 20 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 overall best weight: 11.2090 ------------------------------------------------------------------------------- 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: 0.5737 moved from start: 1.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1159 Z= 0.318 Angle : 0.866 8.001 1611 Z= 0.519 Chirality : 0.050 0.128 221 Planarity : 0.005 0.015 233 Dihedral : 8.918 27.165 233 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.65 % Favored : 78.35 % 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: -5.92 (0.42), residues: 231 helix: -3.46 (0.64), residues: 31 sheet: -3.72 (0.74), residues: 44 loop : -4.41 (0.36), 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 : 0.139 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0168 time to fit residues: 0.2856 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 ------------------------------------------------------------------------------- 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: 30.0000 chunk 20 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 0.4980 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 overall best weight: 4.6786 ------------------------------------------------------------------------------- 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: 0.5651 moved from start: 1.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1159 Z= 0.157 Angle : 0.621 6.573 1611 Z= 0.371 Chirality : 0.048 0.125 221 Planarity : 0.003 0.010 233 Dihedral : 6.938 24.279 233 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % 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: -5.46 (0.46), residues: 231 helix: -2.95 (0.75), residues: 31 sheet: -3.58 (0.72), residues: 46 loop : -4.06 (0.40), residues: 154 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 : 0.142 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0158 time to fit residues: 0.2940 Evaluate side-chains 3 residues out of total 212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 40.0000 chunk 18 optimal weight: 0.0570 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 5 optimal weight: 40.0000 chunk 16 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 7 optimal weight: 0.0030 overall best weight: 1.4512 ------------------------------------------------------------------------------- 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: 0.5557 moved from start: 1.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 1159 Z= 0.083 Angle : 0.487 5.282 1611 Z= 0.290 Chirality : 0.047 0.127 221 Planarity : 0.002 0.008 233 Dihedral : 5.347 22.749 233 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % 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: -5.00 (0.49), residues: 231 helix: -2.49 (0.77), residues: 32 sheet: -3.20 (0.67), residues: 60 loop : -3.75 (0.46), residues: 139 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 : 0.137 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0160 time to fit residues: 0.2965 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 ------------------------------------------------------------------------------- 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: 0.1980 chunk 2 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 chunk 16 optimal weight: 40.0000 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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: 0.5644 moved from start: 1.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1159 Z= 0.141 Angle : 0.564 6.100 1611 Z= 0.335 Chirality : 0.047 0.126 221 Planarity : 0.002 0.009 233 Dihedral : 5.993 24.643 233 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.02 % Favored : 83.98 % 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: -4.99 (0.50), residues: 231 helix: -2.20 (0.80), residues: 32 sheet: -3.10 (0.71), residues: 53 loop : -3.88 (0.46), residues: 146 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 : 0.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0162 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 : 0.137 ------------------------------------------------------------------------------- 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: 30.0000 chunk 22 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 21 optimal weight: 40.0000 chunk 9 optimal weight: 40.0000 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 50.0000 overall best weight: 17.5998 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.079930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.069709 restraints weight = 9058.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.070233 restraints weight = 7792.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.070627 restraints weight = 6958.045| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 1.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 1159 Z= 0.476 Angle : 1.129 8.793 1611 Z= 0.682 Chirality : 0.054 0.129 221 Planarity : 0.007 0.024 233 Dihedral : 10.993 32.678 233 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.57 % Favored : 71.43 % 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 : 0.88 % 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: -6.16 (0.44), residues: 231 helix: -3.92 (0.64), residues: 31 sheet: -2.87 (0.76), residues: 56 loop : -4.97 (0.35), residues: 144 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: 562.31 seconds wall clock time: 10 minutes 37.96 seconds (637.96 seconds total)