Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/11_2022/6tgn_10499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/11_2022/6tgn_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_10499/11_2022/6tgn_10499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/11_2022/6tgn_10499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/11_2022/6tgn_10499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/11_2022/6tgn_10499.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4778/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: 1.36, per 1000 atoms: 2.02 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: 0.22 Conformation dependent library (CDL) restraints added in 133.5 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: 0.05 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: 0.11 Time building geometry restraints manager: 0.26 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 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. 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: 0.360 Check model and map are aligned: 0.020 Convert atoms to be neutral: 0.010 Process input model: 8.570 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 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 % 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 : 0.083 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.1535 time to fit residues: 6.0429 Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.083 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4182 time to fit residues: 0.5375 ------------------------------------------------------------------------------- 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: 8.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 overall best weight: 6.4990 ------------------------------------------------------------------------------- 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: 0.8904 moved from start: 0.4307 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= 0.222 Angle : 0.644 5.753 916 Z= 0.327 Chirality : 0.044 0.134 110 Planarity : 0.003 0.014 120 Dihedral : 4.958 14.093 93 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 8.33 % 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: -2.49 (0.78), residues: 86 helix: -2.95 (0.90), residues: 20 sheet: -1.17 (1.00), residues: 28 loop : -1.06 (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 revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 0.1674 time to fit residues: 6.2452 Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.086 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0133 time to fit residues: 0.1739 ------------------------------------------------------------------------------- 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: 9.9990 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 overall best weight: 11.9995 ------------------------------------------------------------------------------- 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: 0.8941 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.029 678 Z= 0.382 Angle : 0.793 8.515 916 Z= 0.395 Chirality : 0.044 0.119 110 Planarity : 0.004 0.017 120 Dihedral : 5.385 14.360 93 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.94), residues: 86 helix: -2.14 (1.26), residues: 14 sheet: -1.08 (1.03), residues: 28 loop : -0.06 (1.02), residues: 44 *********************** 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 33 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 0.1391 time to fit residues: 4.7695 Evaluate side-chains 26 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.085 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0151 time to fit residues: 0.1363 ------------------------------------------------------------------------------- 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: 20.0000 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 overall best weight: 3.9985 ------------------------------------------------------------------------------- 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: 0.8905 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 678 Z= 0.158 Angle : 0.659 9.016 916 Z= 0.303 Chirality : 0.040 0.121 110 Planarity : 0.002 0.011 120 Dihedral : 4.254 10.520 93 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 4.17 % 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: -0.29 (1.00), residues: 86 helix: -1.20 (1.53), residues: 14 sheet: -1.07 (0.87), residues: 34 loop : 1.48 (1.22), 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 33 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.087 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 31 average time/residue: 0.1498 time to fit residues: 4.9720 Evaluate side-chains 32 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.082 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0136 time to fit residues: 0.1484 ------------------------------------------------------------------------------- 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: 8.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 0.0980 overall best weight: 4.7738 ------------------------------------------------------------------------------- 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: 0.8908 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 678 Z= 0.177 Angle : 0.730 9.092 916 Z= 0.340 Chirality : 0.042 0.119 110 Planarity : 0.002 0.007 120 Dihedral : 4.182 13.271 93 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 5.56 % 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: 0.16 (1.04), residues: 86 helix: -1.49 (1.61), residues: 14 sheet: -0.49 (0.92), residues: 34 loop : 1.73 (1.25), 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 35 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.082 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 0.1384 time to fit residues: 4.8883 Evaluate side-chains 32 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.082 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0120 time to fit residues: 0.1454 ------------------------------------------------------------------------------- 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: 20.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 overall best weight: 9.2490 ------------------------------------------------------------------------------- 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: 0.8939 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.027 678 Z= 0.305 Angle : 0.887 10.432 916 Z= 0.399 Chirality : 0.044 0.140 110 Planarity : 0.003 0.015 120 Dihedral : 4.893 16.452 93 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 6.94 % 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: -0.13 (1.05), residues: 86 helix: -2.12 (1.43), residues: 14 sheet: -0.64 (0.93), residues: 34 loop : 1.68 (1.28), 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 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 32 average time/residue: 0.1454 time to fit residues: 4.9681 Evaluate side-chains 30 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.081 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0134 time to fit residues: 0.1490 ------------------------------------------------------------------------------- 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: 9.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 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: 0.8914 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 678 Z= 0.236 Angle : 0.837 9.307 916 Z= 0.372 Chirality : 0.043 0.138 110 Planarity : 0.002 0.008 120 Dihedral : 4.565 14.506 93 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 4.17 % 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: -0.14 (1.03), residues: 86 helix: -2.05 (1.44), residues: 14 sheet: -0.56 (0.91), residues: 34 loop : 1.55 (1.26), 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 36 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 35 average time/residue: 0.1378 time to fit residues: 5.1719 Evaluate side-chains 31 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.082 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1100 ------------------------------------------------------------------------------- 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: 7.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 overall best weight: 5.2238 ------------------------------------------------------------------------------- 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: 0.8881 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 678 Z= 0.193 Angle : 0.802 8.848 916 Z= 0.350 Chirality : 0.043 0.139 110 Planarity : 0.003 0.017 120 Dihedral : 4.410 13.281 93 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 4.17 % 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: 0.01 (1.01), residues: 86 helix: -2.43 (1.36), residues: 14 sheet: -0.23 (0.92), residues: 34 loop : 1.60 (1.22), 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 37 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.083 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.1340 time to fit residues: 5.0216 Evaluate side-chains 35 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.086 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0127 time to fit residues: 0.1355 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 4.2490 ------------------------------------------------------------------------------- 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: 0.8876 moved from start: 0.6779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 678 Z= 0.193 Angle : 0.807 9.630 916 Z= 0.352 Chirality : 0.043 0.130 110 Planarity : 0.002 0.008 120 Dihedral : 4.104 10.603 93 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.39 % 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: 0.20 (1.02), residues: 86 helix: -1.71 (1.26), residues: 19 sheet: -0.29 (0.90), residues: 34 loop : 2.27 (1.31), residues: 33 *********************** 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 35 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.084 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.1264 time to fit residues: 4.6431 Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.084 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0143 time to fit residues: 0.1346 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 overall best weight: 8.7490 ------------------------------------------------------------------------------- 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: 0.8908 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 678 Z= 0.303 Angle : 0.869 9.470 916 Z= 0.395 Chirality : 0.045 0.141 110 Planarity : 0.004 0.020 120 Dihedral : 4.862 13.953 93 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.39 % 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: -0.55 (0.97), residues: 86 helix: -2.28 (1.08), residues: 20 sheet: -0.56 (0.91), residues: 34 loop : 1.68 (1.25), 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 35 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.084 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.1452 time to fit residues: 5.2741 Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.085 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0114 time to fit residues: 0.1307 ------------------------------------------------------------------------------- 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: 0.0570 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 overall best weight: 3.5380 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.109144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093650 restraints weight = 1473.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.096050 restraints weight = 885.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097723 restraints weight = 631.211| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.7024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 678 Z= 0.192 Angle : 0.852 9.830 916 Z= 0.370 Chirality : 0.043 0.121 110 Planarity : 0.002 0.010 120 Dihedral : 4.261 11.005 93 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (1.01), residues: 86 helix: -2.01 (1.18), residues: 19 sheet: -0.27 (0.93), residues: 34 loop : 2.47 (1.28), residues: 33 =============================================================================== Job complete usr+sys time: 454.23 seconds wall clock time: 8 minutes 50.49 seconds (530.49 seconds total)