Starting phenix.real_space_refine on Thu Dec 7 16:16:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/12_2023/7t2e_25611.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/12_2023/7t2e_25611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/12_2023/7t2e_25611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/12_2023/7t2e_25611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/12_2023/7t2e_25611.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/12_2023/7t2e_25611.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1500 2.51 5 N 404 2.21 5 O 480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2390 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1195 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "B" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1195 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Time building chain proxies: 1.75, per 1000 atoms: 0.73 Number of scatterers: 2390 At special positions: 0 Unit cell: (61.6, 77, 108.9, 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 6 16.00 O 480 8.00 N 404 7.00 C 1500 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: 0.93 Conformation dependent library (CDL) restraints added in 383.9 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 12.8% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 151 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 removed outlier: 5.634A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS A 142 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 127 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR A 140 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS A 129 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR A 138 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 131 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N VAL A 136 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 81 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A 45 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR A 83 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56 removed outlier: 6.681A pdb=" N THR A 51 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 75 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLU A 53 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.506A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS B 142 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 127 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 140 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS B 129 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 138 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 131 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N VAL B 136 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER B 81 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 45 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR B 83 " --> pdb=" O LYS B 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.665A pdb=" N THR B 51 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS B 75 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU B 53 " --> pdb=" O GLY B 73 " (cutoff:3.500A) 78 hydrogen bonds defined for protein. 204 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: 0.54 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: 788 1.34 - 1.46: 564 1.46 - 1.58: 1086 1.58 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 2450 Sorted by residual: bond pdb=" CA GLY A 22 " pdb=" C GLY A 22 " ideal model delta sigma weight residual 1.519 1.512 0.007 8.90e-03 1.26e+04 5.52e-01 bond pdb=" CA ASP A 25 " pdb=" CB ASP A 25 " ideal model delta sigma weight residual 1.528 1.518 0.009 1.50e-02 4.44e+03 3.86e-01 bond pdb=" CG PRO A 113 " pdb=" CD PRO A 113 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.65e-01 bond pdb=" CB LYS A 109 " pdb=" CG LYS A 109 " ideal model delta sigma weight residual 1.520 1.505 0.015 3.00e-02 1.11e+03 2.50e-01 bond pdb=" CA LYS A 21 " pdb=" C LYS A 21 " ideal model delta sigma weight residual 1.523 1.530 -0.008 1.61e-02 3.86e+03 2.33e-01 ... (remaining 2445 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.44: 116 107.44 - 114.08: 1348 114.08 - 120.72: 927 120.72 - 127.37: 911 127.37 - 134.01: 40 Bond angle restraints: 3342 Sorted by residual: angle pdb=" C VAL B 34 " pdb=" N ASP B 35 " pdb=" CA ASP B 35 " ideal model delta sigma weight residual 122.74 125.43 -2.69 1.44e+00 4.82e-01 3.50e+00 angle pdb=" C GLY A 147 " pdb=" N ARG A 148 " pdb=" CA ARG A 148 " ideal model delta sigma weight residual 121.61 124.16 -2.55 1.39e+00 5.18e-01 3.36e+00 angle pdb=" N PHE A 82 " pdb=" CA PHE A 82 " pdb=" C PHE A 82 " ideal model delta sigma weight residual 109.14 111.70 -2.56 1.49e+00 4.50e-01 2.95e+00 angle pdb=" CA TRP B 99 " pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 113.60 116.59 -2.99 1.90e+00 2.77e-01 2.48e+00 angle pdb=" N GLY B 122 " pdb=" CA GLY B 122 " pdb=" C GLY B 122 " ideal model delta sigma weight residual 110.55 113.11 -2.56 1.64e+00 3.72e-01 2.43e+00 ... (remaining 3337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1252 16.87 - 33.73: 130 33.73 - 50.59: 48 50.59 - 67.46: 9 67.46 - 84.32: 1 Dihedral angle restraints: 1440 sinusoidal: 556 harmonic: 884 Sorted by residual: dihedral pdb=" CA ASP A 79 " pdb=" CB ASP A 79 " pdb=" CG ASP A 79 " pdb=" OD1 ASP A 79 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA LYS A 109 " pdb=" C LYS A 109 " pdb=" N ILE A 110 " pdb=" CA ILE A 110 " ideal model delta harmonic sigma weight residual 180.00 164.47 15.53 0 5.00e+00 4.00e-02 9.64e+00 dihedral pdb=" CB GLU B 135 " pdb=" CG GLU B 135 " pdb=" CD GLU B 135 " pdb=" OE1 GLU B 135 " ideal model delta sinusoidal sigma weight residual 0.00 -84.32 84.32 1 3.00e+01 1.11e-03 9.61e+00 ... (remaining 1437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 209 0.028 - 0.057: 95 0.057 - 0.085: 23 0.085 - 0.113: 29 0.113 - 0.141: 8 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ILE A 127 " pdb=" N ILE A 127 " pdb=" C ILE A 127 " pdb=" CB ILE A 127 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE B 127 " pdb=" N ILE B 127 " pdb=" C ILE B 127 " pdb=" CB ILE B 127 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA VAL B 3 " pdb=" N VAL B 3 " pdb=" C VAL B 3 " pdb=" CB VAL B 3 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 361 not shown) Planarity restraints: 434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 112 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 113 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 8 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO A 9 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 8 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.04e-01 pdb=" N PRO B 9 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 9 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 9 " 0.012 5.00e-02 4.00e+02 ... (remaining 431 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 419 2.77 - 3.30: 1887 3.30 - 3.84: 3607 3.84 - 4.37: 3992 4.37 - 4.90: 7404 Nonbonded interactions: 17309 Sorted by model distance: nonbonded pdb=" OH TYR B 108 " pdb=" OD1 ASN B 145 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR A 108 " pdb=" OD1 ASN A 145 " model vdw 2.307 2.440 nonbonded pdb=" O THR A 157 " pdb=" OG1 THR A 157 " model vdw 2.489 2.440 nonbonded pdb=" O SER A 156 " pdb=" OG1 THR A 157 " model vdw 2.498 2.440 nonbonded pdb=" O PRO B 30 " pdb=" NZ LYS B 109 " model vdw 2.538 2.520 ... (remaining 17304 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' } 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: 0.720 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: 3.510 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.270 Find NCS groups from input model: 0.120 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:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.003 0.017 2450 Z= 0.178 Angle : 0.540 4.198 3342 Z= 0.297 Chirality : 0.045 0.141 364 Planarity : 0.004 0.032 434 Dihedral : 16.112 84.321 876 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.18 % Allowed : 22.83 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.45), residues: 308 helix: 1.97 (1.05), residues: 28 sheet: -0.11 (0.39), residues: 158 loop : 0.17 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 18 PHE 0.012 0.002 PHE B 120 TYR 0.009 0.001 TYR A 108 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.255 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 1.4050 time to fit residues: 53.1284 Evaluate side-chains 38 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.1637 time to fit residues: 0.5435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2450 Z= 0.200 Angle : 0.501 4.244 3342 Z= 0.263 Chirality : 0.046 0.147 364 Planarity : 0.004 0.029 434 Dihedral : 4.223 16.026 334 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 22.05 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.47), residues: 308 helix: 2.38 (1.09), residues: 28 sheet: -0.06 (0.40), residues: 158 loop : 0.52 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 PHE 0.013 0.002 PHE A 120 TYR 0.008 0.001 TYR A 108 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.272 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 1.3900 time to fit residues: 55.3223 Evaluate side-chains 39 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.224 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1648 time to fit residues: 0.7306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.0980 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2450 Z= 0.167 Angle : 0.482 4.865 3342 Z= 0.248 Chirality : 0.045 0.145 364 Planarity : 0.003 0.028 434 Dihedral : 4.007 14.898 334 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.97 % Allowed : 22.83 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.47), residues: 308 helix: 2.33 (1.04), residues: 28 sheet: -0.06 (0.40), residues: 158 loop : 0.59 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 18 PHE 0.011 0.002 PHE A 120 TYR 0.008 0.001 TYR A 108 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.279 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 1.3000 time to fit residues: 57.1237 Evaluate side-chains 44 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.249 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.1407 time to fit residues: 0.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2450 Z= 0.299 Angle : 0.549 4.449 3342 Z= 0.287 Chirality : 0.048 0.151 364 Planarity : 0.004 0.034 434 Dihedral : 4.410 15.129 334 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.57 % Allowed : 23.23 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.47), residues: 308 helix: 2.08 (1.04), residues: 28 sheet: -0.13 (0.40), residues: 158 loop : 0.42 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 18 PHE 0.016 0.003 PHE A 120 TYR 0.008 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.269 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 1.4737 time to fit residues: 55.6738 Evaluate side-chains 39 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.1749 time to fit residues: 0.7270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2450 Z= 0.182 Angle : 0.488 5.053 3342 Z= 0.251 Chirality : 0.046 0.145 364 Planarity : 0.003 0.031 434 Dihedral : 4.061 13.603 334 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.97 % Allowed : 23.23 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.47), residues: 308 helix: 2.24 (1.03), residues: 28 sheet: -0.11 (0.40), residues: 158 loop : 0.52 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 18 PHE 0.012 0.002 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.279 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 1.1614 time to fit residues: 53.5596 Evaluate side-chains 39 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1609 time to fit residues: 0.7241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 0.0170 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2450 Z= 0.239 Angle : 0.513 4.361 3342 Z= 0.268 Chirality : 0.046 0.148 364 Planarity : 0.004 0.034 434 Dihedral : 4.222 14.409 334 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.97 % Allowed : 23.62 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.47), residues: 308 helix: 2.18 (1.04), residues: 28 sheet: -0.11 (0.40), residues: 158 loop : 0.44 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 PHE 0.014 0.003 PHE A 120 TYR 0.008 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.290 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 1.4163 time to fit residues: 53.5376 Evaluate side-chains 39 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1786 time to fit residues: 0.7571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 0.0570 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2450 Z= 0.170 Angle : 0.481 5.143 3342 Z= 0.246 Chirality : 0.045 0.143 364 Planarity : 0.003 0.031 434 Dihedral : 3.963 13.216 334 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.57 % Allowed : 23.62 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.47), residues: 308 helix: 2.26 (1.02), residues: 28 sheet: -0.11 (0.40), residues: 158 loop : 0.56 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 18 PHE 0.011 0.002 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.288 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 1.3637 time to fit residues: 52.9805 Evaluate side-chains 38 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1857 time to fit residues: 0.6017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2450 Z= 0.134 Angle : 0.443 4.070 3342 Z= 0.230 Chirality : 0.044 0.140 364 Planarity : 0.003 0.027 434 Dihedral : 3.754 12.308 334 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.97 % Allowed : 23.23 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.47), residues: 308 helix: 2.36 (1.00), residues: 28 sheet: -0.09 (0.40), residues: 158 loop : 0.70 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 18 PHE 0.010 0.002 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.001 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.286 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 1.3917 time to fit residues: 55.4362 Evaluate side-chains 46 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1736 time to fit residues: 0.5386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2450 Z= 0.256 Angle : 0.528 4.357 3342 Z= 0.274 Chirality : 0.047 0.146 364 Planarity : 0.004 0.032 434 Dihedral : 4.228 14.392 334 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.97 % Allowed : 23.62 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.47), residues: 308 helix: 2.19 (1.03), residues: 28 sheet: -0.15 (0.40), residues: 158 loop : 0.52 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 PHE 0.016 0.003 PHE A 120 TYR 0.008 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.280 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 1.4276 time to fit residues: 53.9602 Evaluate side-chains 37 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1672 time to fit residues: 0.5481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2450 Z= 0.333 Angle : 0.594 5.792 3342 Z= 0.304 Chirality : 0.049 0.150 364 Planarity : 0.004 0.037 434 Dihedral : 4.536 15.229 334 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.18 % Allowed : 24.41 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.47), residues: 308 helix: 2.03 (1.03), residues: 28 sheet: -0.19 (0.40), residues: 158 loop : 0.34 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 18 PHE 0.018 0.003 PHE A 120 TYR 0.008 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.285 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 1.5522 time to fit residues: 57.0320 Evaluate side-chains 37 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1898 time to fit residues: 0.5797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.091058 restraints weight = 2951.565| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.16 r_work: 0.2887 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2450 Z= 0.139 Angle : 0.462 4.302 3342 Z= 0.239 Chirality : 0.044 0.141 364 Planarity : 0.003 0.033 434 Dihedral : 3.937 13.642 334 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.79 % Allowed : 24.41 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.48), residues: 308 helix: 2.35 (1.02), residues: 28 sheet: -0.11 (0.40), residues: 158 loop : 0.63 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 18 PHE 0.010 0.002 PHE B 120 TYR 0.006 0.001 TYR A 108 ARG 0.001 0.000 ARG A 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1457.47 seconds wall clock time: 26 minutes 57.78 seconds (1617.78 seconds total)