Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 16:21:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/10_2023/6tgn_10499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/10_2023/6tgn_10499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/10_2023/6tgn_10499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/10_2023/6tgn_10499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/10_2023/6tgn_10499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/10_2023/6tgn_10499.pdb" } resolution = 3.9 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= 1.000 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: 4 Type Number sf(0) Gaussians S 1 5.16 5 C 425 2.51 5 N 115 2.21 5 O 131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 672 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 672 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Time building chain proxies: 0.90, per 1000 atoms: 1.34 Number of scatterers: 672 At special positions: 0 Unit cell: (38.808, 48.51, 51.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 1 16.00 O 131 8.00 N 115 7.00 C 425 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: 0.21 Conformation dependent library (CDL) restraints added in 100.6 milliseconds 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 164 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 2 sheets defined 22.7% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.859A pdb=" N GLU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.864A pdb=" N ASN A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.553A pdb=" N VAL A 17 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 14 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.553A pdb=" N VAL A 17 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 14 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 13 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 89 " --> pdb=" O SER A 13 " (cutoff:3.500A) 17 hydrogen bonds defined for protein. 42 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: 0.13 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 124 1.32 - 1.44: 153 1.44 - 1.56: 399 1.56 - 1.68: 0 1.68 - 1.80: 2 Bond restraints: 678 Sorted by residual: bond pdb=" C TYR A 58 " pdb=" O TYR A 58 " ideal model delta sigma weight residual 1.234 1.197 0.037 1.16e-02 7.43e+03 1.01e+01 bond pdb=" CA ILE A 87 " pdb=" CB ILE A 87 " ideal model delta sigma weight residual 1.537 1.505 0.032 1.26e-02 6.30e+03 6.49e+00 bond pdb=" N ALA A 5 " pdb=" CA ALA A 5 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.31e+00 bond pdb=" C LEU A 56 " pdb=" O LEU A 56 " ideal model delta sigma weight residual 1.236 1.209 0.026 1.21e-02 6.83e+03 4.72e+00 bond pdb=" C ILE A 87 " pdb=" O ILE A 87 " ideal model delta sigma weight residual 1.238 1.214 0.024 1.10e-02 8.26e+03 4.64e+00 ... (remaining 673 not shown) Histogram of bond angle deviations from ideal: 100.47 - 105.68: 7 105.68 - 110.90: 208 110.90 - 116.11: 238 116.11 - 121.33: 292 121.33 - 126.54: 171 Bond angle restraints: 916 Sorted by residual: angle pdb=" C ASN A 88 " pdb=" CA ASN A 88 " pdb=" CB ASN A 88 " ideal model delta sigma weight residual 109.53 102.18 7.35 1.65e+00 3.67e-01 1.98e+01 angle pdb=" O GLY A 15 " pdb=" C GLY A 15 " pdb=" N GLY A 16 " ideal model delta sigma weight residual 122.57 126.54 -3.97 9.10e-01 1.21e+00 1.90e+01 angle pdb=" N ILE A 87 " pdb=" CA ILE A 87 " pdb=" C ILE A 87 " ideal model delta sigma weight residual 107.75 113.41 -5.66 1.46e+00 4.69e-01 1.50e+01 angle pdb=" CA LYS A 11 " pdb=" C LYS A 11 " pdb=" O LYS A 11 " ideal model delta sigma weight residual 120.32 116.14 4.18 1.10e+00 8.26e-01 1.44e+01 angle pdb=" N LEU A 85 " pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " ideal model delta sigma weight residual 110.29 105.20 5.09 1.52e+00 4.33e-01 1.12e+01 ... (remaining 911 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.12: 333 10.12 - 20.23: 57 20.23 - 30.34: 15 30.34 - 40.45: 4 40.45 - 50.55: 3 Dihedral angle restraints: 412 sinusoidal: 159 harmonic: 253 Sorted by residual: dihedral pdb=" CA ASP A 62 " pdb=" C ASP A 62 " pdb=" N GLY A 63 " pdb=" CA GLY A 63 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ALA A 5 " pdb=" C ALA A 5 " pdb=" N ASN A 6 " pdb=" CA ASN A 6 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C ASN A 88 " pdb=" N ASN A 88 " pdb=" CA ASN A 88 " pdb=" CB ASN A 88 " ideal model delta harmonic sigma weight residual -122.60 -112.69 -9.91 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 409 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.058: 41 0.058 - 0.115: 36 0.115 - 0.172: 17 0.172 - 0.229: 10 0.229 - 0.286: 6 Chirality restraints: 110 Sorted by residual: chirality pdb=" CA VAL A 66 " pdb=" N VAL A 66 " pdb=" C VAL A 66 " pdb=" CB VAL A 66 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ARG A 81 " pdb=" N ARG A 81 " pdb=" C ARG A 81 " pdb=" CB ARG A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR A 58 " pdb=" N TYR A 58 " pdb=" C TYR A 58 " pdb=" CB TYR A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 107 not shown) Planarity restraints: 120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 14 " 0.042 2.00e-02 2.50e+03 2.17e-02 9.38e+00 pdb=" CG TYR A 14 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 14 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 14 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 14 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 14 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 14 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 14 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 58 " -0.030 2.00e-02 2.50e+03 1.63e-02 5.33e+00 pdb=" CG TYR A 58 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 58 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 58 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 58 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 58 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 58 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 58 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 46 " 0.001 2.00e-02 2.50e+03 1.71e-02 5.12e+00 pdb=" CG PHE A 46 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 46 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 46 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 46 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 46 " -0.019 2.00e-02 2.50e+03 ... (remaining 117 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 41 2.71 - 3.26: 598 3.26 - 3.80: 901 3.80 - 4.35: 1146 4.35 - 4.90: 1881 Nonbonded interactions: 4567 Sorted by model distance: nonbonded pdb=" OD1 ASP A 60 " pdb=" N GLU A 61 " model vdw 2.161 2.520 nonbonded pdb=" N ASP A 60 " pdb=" O ASP A 60 " model vdw 2.548 2.496 nonbonded pdb=" N ARG A 19 " pdb=" O ARG A 19 " model vdw 2.602 2.496 nonbonded pdb=" N GLU A 34 " pdb=" OE1 GLU A 34 " model vdw 2.607 2.520 nonbonded pdb=" O ARG A 19 " pdb=" CA ARG A 20 " model vdw 2.627 2.776 ... (remaining 4562 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: 0.070 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.580 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 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 : 0.010 0.044 678 Z= 0.599 Angle : 1.727 7.656 916 Z= 1.087 Chirality : 0.118 0.286 110 Planarity : 0.008 0.022 120 Dihedral : 11.933 50.555 248 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 2.78 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.75), residues: 86 helix: -4.95 (0.26), residues: 18 sheet: -1.43 (0.99), residues: 28 loop : -1.61 (0.75), residues: 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.080 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.1477 time to fit residues: 5.7957 Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.078 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4180 time to fit residues: 0.5291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 overall best weight: 5.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 678 Z= 0.197 Angle : 0.640 5.695 916 Z= 0.322 Chirality : 0.044 0.133 110 Planarity : 0.003 0.013 120 Dihedral : 4.837 13.878 93 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 8.33 % Allowed : 15.28 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.78), residues: 86 helix: -2.95 (0.90), residues: 20 sheet: -1.15 (0.99), residues: 28 loop : -1.04 (0.76), residues: 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.083 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 0.1366 time to fit residues: 5.1164 Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.072 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0136 time to fit residues: 0.1603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- 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: 0.8832 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 678 Z= 0.241 Angle : 0.703 8.560 916 Z= 0.338 Chirality : 0.042 0.124 110 Planarity : 0.003 0.012 120 Dihedral : 4.762 13.402 93 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.39 % Allowed : 27.78 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.93), residues: 86 helix: -2.11 (1.25), residues: 14 sheet: -1.30 (0.87), residues: 34 loop : 0.94 (1.08), residues: 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.075 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.1493 time to fit residues: 4.7558 Evaluate side-chains 24 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.080 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 overall best weight: 4.6238 ------------------------------------------------------------------------------- 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: 0.8805 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 678 Z= 0.178 Angle : 0.655 8.718 916 Z= 0.304 Chirality : 0.040 0.122 110 Planarity : 0.002 0.012 120 Dihedral : 4.098 10.127 93 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.17 % Allowed : 27.78 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.97), residues: 86 helix: -1.49 (1.44), residues: 14 sheet: -1.04 (0.85), residues: 34 loop : 1.50 (1.15), residues: 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.050 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.1072 time to fit residues: 3.7760 Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.055 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0094 time to fit residues: 0.1160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 overall best weight: 6.7490 ------------------------------------------------------------------------------- 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: 0.8811 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 678 Z= 0.228 Angle : 0.739 8.880 916 Z= 0.342 Chirality : 0.042 0.122 110 Planarity : 0.002 0.010 120 Dihedral : 4.170 11.135 93 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.78 % Allowed : 29.17 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (1.00), residues: 86 helix: -2.06 (1.33), residues: 14 sheet: -0.74 (0.86), residues: 34 loop : 1.75 (1.23), residues: 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.088 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.1556 time to fit residues: 5.3176 Evaluate side-chains 33 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.077 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0133 time to fit residues: 0.1736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 overall best weight: 8.2490 ------------------------------------------------------------------------------- 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: 0.8843 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 678 Z= 0.266 Angle : 0.804 9.134 916 Z= 0.368 Chirality : 0.044 0.121 110 Planarity : 0.003 0.014 120 Dihedral : 4.474 12.770 93 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.39 % Allowed : 30.56 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (1.05), residues: 86 helix: -2.51 (1.42), residues: 14 sheet: -0.73 (0.91), residues: 34 loop : 1.83 (1.27), residues: 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.084 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.1622 time to fit residues: 5.3497 Evaluate side-chains 31 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.082 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0147 time to fit residues: 0.1311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 0.0170 chunk 7 optimal weight: 7.9990 overall best weight: 4.7535 ------------------------------------------------------------------------------- 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: 0.8819 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 678 Z= 0.203 Angle : 0.838 8.483 916 Z= 0.365 Chirality : 0.044 0.122 110 Planarity : 0.002 0.010 120 Dihedral : 4.612 14.134 93 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.39 % Allowed : 34.72 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (1.04), residues: 86 helix: -2.66 (1.32), residues: 14 sheet: -0.45 (0.92), residues: 34 loop : 1.90 (1.28), residues: 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.078 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.1456 time to fit residues: 5.1269 Evaluate side-chains 32 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.8824 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 678 Z= 0.243 Angle : 0.881 9.303 916 Z= 0.384 Chirality : 0.046 0.147 110 Planarity : 0.003 0.018 120 Dihedral : 4.853 15.920 93 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 5.56 % Allowed : 31.94 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (1.05), residues: 86 helix: -2.62 (1.38), residues: 14 sheet: -0.38 (0.92), residues: 34 loop : 1.85 (1.28), residues: 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.081 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 0.1532 time to fit residues: 5.3870 Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.078 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0124 time to fit residues: 0.1610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 overall best weight: 7.0235 ------------------------------------------------------------------------------- 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: 0.8794 moved from start: 0.6934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 678 Z= 0.264 Angle : 0.983 9.328 916 Z= 0.440 Chirality : 0.049 0.141 110 Planarity : 0.002 0.009 120 Dihedral : 5.103 19.229 93 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 34.72 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.97), residues: 86 helix: -2.72 (0.98), residues: 20 sheet: -0.37 (0.90), residues: 34 loop : 1.50 (1.30), residues: 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1557 time to fit residues: 5.3059 Evaluate side-chains 31 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.081 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 0.0010 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.4993 ------------------------------------------------------------------------------- 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: 0.8782 moved from start: 0.6947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 678 Z= 0.195 Angle : 0.908 9.353 916 Z= 0.392 Chirality : 0.044 0.129 110 Planarity : 0.003 0.016 120 Dihedral : 4.343 12.832 93 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.39 % Allowed : 36.11 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.98), residues: 86 helix: -2.42 (1.07), residues: 20 sheet: -0.10 (0.92), residues: 34 loop : 1.66 (1.26), residues: 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.091 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.1581 time to fit residues: 5.2270 Evaluate side-chains 32 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.068 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0137 time to fit residues: 0.1229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.0170 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 overall best weight: 4.2535 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092014 restraints weight = 1513.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094065 restraints weight = 936.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095499 restraints weight = 679.923| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.7113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 678 Z= 0.215 Angle : 0.917 9.329 916 Z= 0.400 Chirality : 0.044 0.126 110 Planarity : 0.003 0.014 120 Dihedral : 4.397 15.496 93 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.39 % Allowed : 34.72 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.98), residues: 86 helix: -2.38 (1.06), residues: 20 sheet: 0.03 (0.93), residues: 34 loop : 1.71 (1.26), residues: 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 441.68 seconds wall clock time: 15 minutes 46.44 seconds (946.44 seconds total)