Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 19 23:14:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/04_2023/7tik_25912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/04_2023/7tik_25912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/04_2023/7tik_25912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/04_2023/7tik_25912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/04_2023/7tik_25912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/04_2023/7tik_25912.pdb" } resolution = 2.4 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1584 2.51 5 N 450 2.21 5 O 531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 2565 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "E" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "F" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Time building chain proxies: 1.74, per 1000 atoms: 0.68 Number of scatterers: 2565 At special positions: 0 Unit cell: (52, 42.25, 118.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 531 8.00 N 450 7.00 C 1584 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: 1.04 Conformation dependent library (CDL) restraints added in 448.4 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 removed outlier: 3.618A pdb=" N LEU D1197 " --> pdb=" O ASN D1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1194 through 1197' Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 removed outlier: 3.618A pdb=" N LEU E1197 " --> pdb=" O ASN E1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1194 through 1197' Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 removed outlier: 3.618A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 232 hydrogen bonds defined for protein. 696 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: 0.68 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 480 1.29 - 1.35: 420 1.35 - 1.41: 89 1.41 - 1.48: 382 1.48 - 1.54: 1206 Bond restraints: 2577 Sorted by residual: bond pdb=" CA LEU C 966 " pdb=" C LEU C 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.44e-01 bond pdb=" CA LEU B 966 " pdb=" C LEU B 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.25e-01 bond pdb=" CB ASN C 955 " pdb=" CG ASN C 955 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 8.08e-01 bond pdb=" CA LEU A 966 " pdb=" C LEU A 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.00e-01 bond pdb=" CA LEU B 962 " pdb=" C LEU B 962 " ideal model delta sigma weight residual 1.524 1.512 0.011 1.29e-02 6.01e+03 7.82e-01 ... (remaining 2572 not shown) Histogram of bond angle deviations from ideal: 103.19 - 108.80: 64 108.80 - 114.42: 1608 114.42 - 120.03: 744 120.03 - 125.65: 1052 125.65 - 131.27: 9 Bond angle restraints: 3477 Sorted by residual: angle pdb=" CA ILE B 980 " pdb=" CB ILE B 980 " pdb=" CG1 ILE B 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.59e+00 angle pdb=" CA ILE A 980 " pdb=" CB ILE A 980 " pdb=" CG1 ILE A 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.56e+00 angle pdb=" CA ILE C 980 " pdb=" CB ILE C 980 " pdb=" CG1 ILE C 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.56e+00 angle pdb=" C ASP C 979 " pdb=" N ILE C 980 " pdb=" CA ILE C 980 " ideal model delta sigma weight residual 120.64 115.62 5.02 1.64e+00 3.72e-01 9.39e+00 angle pdb=" C ASP B 979 " pdb=" N ILE B 980 " pdb=" CA ILE B 980 " ideal model delta sigma weight residual 120.64 115.64 5.00 1.64e+00 3.72e-01 9.29e+00 ... (remaining 3472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1404 17.40 - 34.81: 159 34.81 - 52.21: 21 52.21 - 69.61: 12 69.61 - 87.02: 6 Dihedral angle restraints: 1602 sinusoidal: 621 harmonic: 981 Sorted by residual: dihedral pdb=" CA ASN F1192 " pdb=" CB ASN F1192 " pdb=" CG ASN F1192 " pdb=" OD1 ASN F1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.29 -71.71 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN D1192 " pdb=" CB ASN D1192 " pdb=" CG ASN D1192 " pdb=" OD1 ASN D1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.31 -71.69 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN E1192 " pdb=" CB ASN E1192 " pdb=" CG ASN E1192 " pdb=" OD1 ASN E1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.33 -71.67 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 1599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 210 0.028 - 0.056: 165 0.056 - 0.084: 33 0.084 - 0.112: 7 0.112 - 0.140: 17 Chirality restraints: 432 Sorted by residual: chirality pdb=" CB ILE B 980 " pdb=" CA ILE B 980 " pdb=" CG1 ILE B 980 " pdb=" CG2 ILE B 980 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CB ILE A 980 " pdb=" CA ILE A 980 " pdb=" CG1 ILE A 980 " pdb=" CG2 ILE A 980 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL E1176 " pdb=" N VAL E1176 " pdb=" C VAL E1176 " pdb=" CB VAL E1176 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 429 not shown) Planarity restraints: 456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 981 " 0.007 2.00e-02 2.50e+03 9.97e-03 1.74e+00 pdb=" CG PHE A 981 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 981 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 981 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 981 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 981 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 981 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 981 " -0.007 2.00e-02 2.50e+03 9.81e-03 1.68e+00 pdb=" CG PHE B 981 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 981 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 981 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 981 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 981 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 981 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 981 " -0.007 2.00e-02 2.50e+03 9.74e-03 1.66e+00 pdb=" CG PHE C 981 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 981 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 981 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 981 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 981 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 981 " -0.000 2.00e-02 2.50e+03 ... (remaining 453 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 463 2.75 - 3.29: 2698 3.29 - 3.83: 4418 3.83 - 4.36: 4841 4.36 - 4.90: 8357 Nonbonded interactions: 20777 Sorted by model distance: nonbonded pdb=" OG SER A 943 " pdb=" OE2 GLU F1182 " model vdw 2.218 2.440 nonbonded pdb=" OD2 ASP A 936 " pdb=" NH2 ARG F1185 " model vdw 2.259 2.520 nonbonded pdb=" O LYS B 964 " pdb=" OG SER B 967 " model vdw 2.283 2.440 nonbonded pdb=" O LYS A 964 " pdb=" OG SER A 967 " model vdw 2.283 2.440 nonbonded pdb=" O LYS C 964 " pdb=" OG SER C 967 " model vdw 2.283 2.440 ... (remaining 20772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.480 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.580 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.007 0.027 2577 Z= 0.418 Angle : 0.491 5.265 3477 Z= 0.283 Chirality : 0.042 0.140 432 Planarity : 0.003 0.016 456 Dihedral : 16.305 87.018 954 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: 1.31 (0.41), residues: 327 helix: 1.84 (0.28), residues: 252 sheet: None (None), residues: 0 loop : -2.67 (0.54), residues: 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.308 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.5936 time to fit residues: 33.7753 Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.0870 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN B 960 ASN C 960 ASN D1192 ASN E1192 ASN F1192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 2577 Z= 0.180 Angle : 0.388 7.033 3477 Z= 0.208 Chirality : 0.037 0.132 432 Planarity : 0.002 0.011 456 Dihedral : 3.329 12.788 339 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.44), residues: 327 helix: 4.00 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -1.09 (0.69), residues: 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.311 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.6116 time to fit residues: 33.4026 Evaluate side-chains 51 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 2577 Z= 0.199 Angle : 0.373 5.450 3477 Z= 0.201 Chirality : 0.037 0.131 432 Planarity : 0.002 0.009 456 Dihedral : 3.067 12.446 339 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.14 (0.45), residues: 327 helix: 4.48 (0.28), residues: 252 sheet: None (None), residues: 0 loop : -0.88 (0.71), residues: 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.320 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.6319 time to fit residues: 33.8187 Evaluate side-chains 51 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.0830 time to fit residues: 0.5852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN B 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 2577 Z= 0.233 Angle : 0.373 4.482 3477 Z= 0.211 Chirality : 0.037 0.134 432 Planarity : 0.002 0.015 456 Dihedral : 3.120 11.707 339 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.26 (0.45), residues: 327 helix: 4.54 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.73 (0.74), residues: 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.293 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.6356 time to fit residues: 34.7570 Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.6657 time to fit residues: 1.8090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2577 Z= 0.201 Angle : 0.400 5.512 3477 Z= 0.221 Chirality : 0.037 0.142 432 Planarity : 0.002 0.025 456 Dihedral : 3.071 11.067 339 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.43 (0.45), residues: 327 helix: 4.63 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.56 (0.75), residues: 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.304 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.6164 time to fit residues: 33.6544 Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0284 time to fit residues: 0.4927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2577 Z= 0.216 Angle : 0.396 5.655 3477 Z= 0.228 Chirality : 0.038 0.144 432 Planarity : 0.002 0.029 456 Dihedral : 3.088 11.303 339 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.33 (0.45), residues: 327 helix: 4.53 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.46 (0.76), residues: 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.293 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.6233 time to fit residues: 33.4725 Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0275 time to fit residues: 0.5189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 2577 Z= 0.229 Angle : 0.424 6.262 3477 Z= 0.234 Chirality : 0.038 0.150 432 Planarity : 0.002 0.025 456 Dihedral : 3.100 11.622 339 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.37 (0.45), residues: 327 helix: 4.53 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.34 (0.78), residues: 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.273 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.6111 time to fit residues: 33.3505 Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.6922 time to fit residues: 1.8819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 0.0170 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.0370 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN E1159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 2577 Z= 0.157 Angle : 0.389 6.320 3477 Z= 0.224 Chirality : 0.037 0.171 432 Planarity : 0.002 0.025 456 Dihedral : 3.003 12.685 339 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.65 (0.45), residues: 327 helix: 4.72 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.19 (0.79), residues: 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.313 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.6123 time to fit residues: 32.8129 Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0287 time to fit residues: 0.4931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 26 optimal weight: 0.0980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN F1159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 2577 Z= 0.181 Angle : 0.432 6.877 3477 Z= 0.238 Chirality : 0.037 0.159 432 Planarity : 0.002 0.026 456 Dihedral : 3.042 13.909 339 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.71 (0.45), residues: 327 helix: 4.76 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.15 (0.79), residues: 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.286 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.6200 time to fit residues: 33.7923 Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2577 Z= 0.218 Angle : 0.421 5.912 3477 Z= 0.240 Chirality : 0.038 0.164 432 Planarity : 0.002 0.026 456 Dihedral : 3.159 14.712 339 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.64 (0.45), residues: 327 helix: 4.72 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.22 (0.79), residues: 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.318 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 55 average time/residue: 0.6260 time to fit residues: 36.1056 Evaluate side-chains 55 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.144869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.122613 restraints weight = 3519.302| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.10 r_work: 0.3954 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2577 Z= 0.195 Angle : 0.449 6.962 3477 Z= 0.256 Chirality : 0.038 0.147 432 Planarity : 0.002 0.030 456 Dihedral : 3.169 14.319 339 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.52 (0.45), residues: 327 helix: 4.62 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.19 (0.79), residues: 75 =============================================================================== Job complete usr+sys time: 1247.17 seconds wall clock time: 22 minutes 53.85 seconds (1373.85 seconds total)