Starting phenix.real_space_refine on Thu Dec 7 16:12:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/12_2023/8g3k_29700.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/12_2023/8g3k_29700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/12_2023/8g3k_29700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/12_2023/8g3k_29700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/12_2023/8g3k_29700.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3k_29700/12_2023/8g3k_29700.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1425 2.51 5 N 386 2.21 5 O 423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2244 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1069 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1175 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Time building chain proxies: 1.78, per 1000 atoms: 0.79 Number of scatterers: 2244 At special positions: 0 Unit cell: (56, 72, 73, 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 10 16.00 O 423 8.00 N 386 7.00 C 1425 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: 0.92 Conformation dependent library (CDL) restraints added in 440.0 milliseconds 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.692A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 136 Processing helix chain 'A' and resid 138 through 165 Processing helix chain 'B' and resid 24 through 46 Processing helix chain 'B' and resid 48 through 72 Processing helix chain 'B' and resid 79 through 98 removed outlier: 3.678A pdb=" N ILE B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 134 removed outlier: 3.579A pdb=" N GLU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 171 removed outlier: 4.001A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 603 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: 0.62 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 749 1.34 - 1.46: 322 1.46 - 1.58: 1177 1.58 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 2267 Sorted by residual: bond pdb=" C ALA A 146 " pdb=" O ALA A 146 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.15e-02 7.56e+03 3.71e-01 bond pdb=" CG1 ILE A 120 " pdb=" CD1 ILE A 120 " ideal model delta sigma weight residual 1.513 1.489 0.024 3.90e-02 6.57e+02 3.69e-01 bond pdb=" C ASP A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.36e-02 5.41e+03 3.60e-01 bond pdb=" C PHE B 56 " pdb=" O PHE B 56 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.19e-02 7.06e+03 3.51e-01 bond pdb=" C ASP B 61 " pdb=" O ASP B 61 " ideal model delta sigma weight residual 1.236 1.229 0.007 1.26e-02 6.30e+03 3.19e-01 ... (remaining 2262 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 30 107.11 - 113.82: 1325 113.82 - 120.54: 908 120.54 - 127.25: 769 127.25 - 133.97: 11 Bond angle restraints: 3043 Sorted by residual: angle pdb=" CA LEU B 43 " pdb=" CB LEU B 43 " pdb=" CG LEU B 43 " ideal model delta sigma weight residual 116.30 121.09 -4.79 3.50e+00 8.16e-02 1.88e+00 angle pdb=" CA TRP A 86 " pdb=" CB TRP A 86 " pdb=" CG TRP A 86 " ideal model delta sigma weight residual 113.60 115.97 -2.37 1.90e+00 2.77e-01 1.56e+00 angle pdb=" C ASP A 25 " pdb=" N PRO A 26 " pdb=" CD PRO A 26 " ideal model delta sigma weight residual 125.00 129.81 -4.81 4.10e+00 5.95e-02 1.38e+00 angle pdb=" N GLY A 138 " pdb=" CA GLY A 138 " pdb=" C GLY A 138 " ideal model delta sigma weight residual 113.18 115.93 -2.75 2.37e+00 1.78e-01 1.34e+00 angle pdb=" C VAL B 64 " pdb=" N LEU B 65 " pdb=" CA LEU B 65 " ideal model delta sigma weight residual 120.29 121.61 -1.32 1.42e+00 4.96e-01 8.65e-01 ... (remaining 3038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1349 17.96 - 35.93: 38 35.93 - 53.89: 9 53.89 - 71.85: 2 71.85 - 89.82: 1 Dihedral angle restraints: 1399 sinusoidal: 582 harmonic: 817 Sorted by residual: dihedral pdb=" CB ARG B 127 " pdb=" CG ARG B 127 " pdb=" CD ARG B 127 " pdb=" NE ARG B 127 " ideal model delta sinusoidal sigma weight residual -60.00 -112.92 52.92 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" CA ARG A 122 " pdb=" CB ARG A 122 " pdb=" CG ARG A 122 " pdb=" CD ARG A 122 " ideal model delta sinusoidal sigma weight residual -60.00 -106.90 46.90 3 1.50e+01 4.44e-03 8.41e+00 dihedral pdb=" N GLU A 134 " pdb=" CA GLU A 134 " pdb=" CB GLU A 134 " pdb=" CG GLU A 134 " ideal model delta sinusoidal sigma weight residual -180.00 -137.08 -42.92 3 1.50e+01 4.44e-03 7.71e+00 ... (remaining 1396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 246 0.025 - 0.049: 60 0.049 - 0.074: 36 0.074 - 0.098: 10 0.098 - 0.123: 6 Chirality restraints: 358 Sorted by residual: chirality pdb=" CA ILE B 138 " pdb=" N ILE B 138 " pdb=" C ILE B 138 " pdb=" CB ILE B 138 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE A 76 " pdb=" N ILE A 76 " pdb=" C ILE A 76 " pdb=" CB ILE A 76 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA ILE A 137 " pdb=" N ILE A 137 " pdb=" C ILE A 137 " pdb=" CB ILE A 137 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 355 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 145 " -0.009 2.00e-02 2.50e+03 4.88e-03 4.76e-01 pdb=" CG TYR B 145 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 145 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 145 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 145 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 145 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 145 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 38 " 0.003 2.00e-02 2.50e+03 6.22e-03 3.86e-01 pdb=" C THR A 38 " -0.011 2.00e-02 2.50e+03 pdb=" O THR A 38 " 0.004 2.00e-02 2.50e+03 pdb=" N SER A 39 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 86 " -0.006 2.00e-02 2.50e+03 3.83e-03 3.66e-01 pdb=" CG TRP A 86 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 86 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 86 " 0.000 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 739 2.86 - 3.37: 2386 3.37 - 3.88: 3896 3.88 - 4.39: 4210 4.39 - 4.90: 7179 Nonbonded interactions: 18410 Sorted by model distance: nonbonded pdb=" OD1 ASP B 49 " pdb=" NH2 ARG B 52 " model vdw 2.348 2.520 nonbonded pdb=" O ILE A 91 " pdb=" OG SER A 95 " model vdw 2.386 2.440 nonbonded pdb=" OE2 GLU A 81 " pdb=" ND2 ASN B 151 " model vdw 2.403 2.520 nonbonded pdb=" OE2 GLU B 126 " pdb=" OG SER B 150 " model vdw 2.478 2.440 nonbonded pdb=" O GLU A 57 " pdb=" ND2 ASN A 61 " model vdw 2.493 2.520 ... (remaining 18405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.970 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.320 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.002 0.024 2267 Z= 0.123 Angle : 0.357 4.810 3043 Z= 0.191 Chirality : 0.033 0.123 358 Planarity : 0.002 0.016 384 Dihedral : 9.977 89.815 871 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.07 (0.45), residues: 279 helix: 3.75 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 1.02 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 86 HIS 0.001 0.000 HIS A 46 PHE 0.003 0.001 PHE B 154 TYR 0.009 0.001 TYR B 145 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.273 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 1.6606 time to fit residues: 143.1478 Evaluate side-chains 59 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 139 ASN B 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2267 Z= 0.165 Angle : 0.403 4.837 3043 Z= 0.219 Chirality : 0.034 0.122 358 Planarity : 0.003 0.019 384 Dihedral : 3.276 10.979 309 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.88 % Allowed : 10.70 % Favored : 86.42 % 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: 4.97 (0.45), residues: 279 helix: 3.67 (0.29), residues: 234 sheet: None (None), residues: 0 loop : 0.89 (0.91), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 48 HIS 0.001 0.001 HIS B 156 PHE 0.006 0.001 PHE A 135 TYR 0.010 0.002 TYR B 145 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.264 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 61 average time/residue: 1.7196 time to fit residues: 106.4322 Evaluate side-chains 60 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0249 time to fit residues: 0.4189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 0.0040 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2267 Z= 0.159 Angle : 0.405 4.858 3043 Z= 0.219 Chirality : 0.034 0.121 358 Planarity : 0.003 0.020 384 Dihedral : 3.282 11.037 309 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.65 % Allowed : 12.76 % Favored : 85.60 % 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: 4.83 (0.46), residues: 279 helix: 3.60 (0.29), residues: 235 sheet: None (None), residues: 0 loop : 0.58 (0.91), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.004 0.001 PHE A 40 TYR 0.011 0.002 TYR B 145 ARG 0.002 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.265 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 61 average time/residue: 1.7547 time to fit residues: 108.6036 Evaluate side-chains 57 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.246 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 21 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2267 Z= 0.138 Angle : 0.400 6.166 3043 Z= 0.213 Chirality : 0.033 0.123 358 Planarity : 0.002 0.017 384 Dihedral : 3.242 10.715 309 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.65 % Allowed : 12.35 % Favored : 86.01 % 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: 4.88 (0.46), residues: 279 helix: 3.61 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.64 (0.92), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 48 HIS 0.001 0.001 HIS B 156 PHE 0.003 0.000 PHE A 40 TYR 0.010 0.002 TYR B 145 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.259 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 1.6643 time to fit residues: 103.0481 Evaluate side-chains 58 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0254 time to fit residues: 0.4163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 15 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2267 Z= 0.234 Angle : 0.477 6.990 3043 Z= 0.251 Chirality : 0.037 0.123 358 Planarity : 0.003 0.024 384 Dihedral : 3.460 12.464 309 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 13.58 % Favored : 84.36 % 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: 4.65 (0.45), residues: 279 helix: 3.52 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.51 (0.87), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 48 HIS 0.002 0.001 HIS B 116 PHE 0.006 0.001 PHE A 40 TYR 0.016 0.002 TYR B 85 ARG 0.002 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.262 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 63 average time/residue: 1.6711 time to fit residues: 106.9342 Evaluate side-chains 60 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2267 Z= 0.134 Angle : 0.413 7.800 3043 Z= 0.219 Chirality : 0.033 0.122 358 Planarity : 0.002 0.015 384 Dihedral : 3.234 10.849 309 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.23 % Allowed : 16.46 % Favored : 82.30 % 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: 4.97 (0.45), residues: 279 helix: 3.69 (0.29), residues: 233 sheet: None (None), residues: 0 loop : 0.81 (0.90), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.003 0.000 PHE A 135 TYR 0.010 0.001 TYR B 85 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.274 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 1.7075 time to fit residues: 102.2980 Evaluate side-chains 58 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0263 time to fit residues: 0.4354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.0000 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2267 Z= 0.154 Angle : 0.439 8.342 3043 Z= 0.231 Chirality : 0.034 0.123 358 Planarity : 0.002 0.015 384 Dihedral : 3.226 10.982 309 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.41 % Allowed : 16.05 % Favored : 83.54 % 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: 4.87 (0.45), residues: 279 helix: 3.63 (0.29), residues: 234 sheet: None (None), residues: 0 loop : 0.63 (0.90), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 48 HIS 0.001 0.001 HIS B 156 PHE 0.003 0.001 PHE A 135 TYR 0.009 0.001 TYR B 145 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.246 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 1.7759 time to fit residues: 104.5458 Evaluate side-chains 59 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2267 Z= 0.188 Angle : 0.464 9.275 3043 Z= 0.241 Chirality : 0.035 0.119 358 Planarity : 0.003 0.017 384 Dihedral : 3.350 11.870 309 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.23 % Allowed : 16.46 % Favored : 82.30 % 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: 4.74 (0.45), residues: 279 helix: 3.58 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.54 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 48 HIS 0.001 0.001 HIS B 156 PHE 0.004 0.001 PHE A 40 TYR 0.011 0.002 TYR B 145 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.283 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 61 average time/residue: 1.7681 time to fit residues: 109.3921 Evaluate side-chains 60 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2267 Z= 0.172 Angle : 0.464 9.473 3043 Z= 0.245 Chirality : 0.034 0.119 358 Planarity : 0.002 0.015 384 Dihedral : 3.354 11.338 309 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.82 % Allowed : 16.87 % Favored : 82.30 % 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: 4.69 (0.45), residues: 279 helix: 3.59 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.25 (0.86), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 48 HIS 0.001 0.001 HIS B 156 PHE 0.006 0.001 PHE A 135 TYR 0.010 0.002 TYR B 145 ARG 0.001 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.253 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 1.7972 time to fit residues: 109.4235 Evaluate side-chains 59 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2267 Z= 0.202 Angle : 0.487 9.948 3043 Z= 0.252 Chirality : 0.035 0.117 358 Planarity : 0.003 0.017 384 Dihedral : 3.390 12.155 309 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.41 % Allowed : 17.70 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.45), residues: 279 helix: 3.49 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.25 (0.87), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP B 48 HIS 0.001 0.001 HIS B 156 PHE 0.005 0.001 PHE A 40 TYR 0.012 0.002 TYR B 145 ARG 0.001 0.000 ARG B 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.280 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 1.7810 time to fit residues: 110.2478 Evaluate side-chains 61 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.150557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124894 restraints weight = 2033.764| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.20 r_work: 0.3252 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2267 Z= 0.150 Angle : 0.456 10.491 3043 Z= 0.234 Chirality : 0.034 0.119 358 Planarity : 0.002 0.014 384 Dihedral : 3.272 10.983 309 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.41 % Allowed : 18.52 % Favored : 81.07 % 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: 4.77 (0.46), residues: 279 helix: 3.59 (0.29), residues: 233 sheet: None (None), residues: 0 loop : 0.52 (0.92), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP B 48 HIS 0.001 0.001 HIS B 156 PHE 0.009 0.001 PHE A 135 TYR 0.009 0.001 TYR B 145 ARG 0.001 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.83 seconds wall clock time: 35 minutes 26.64 seconds (2126.64 seconds total)