Starting phenix.real_space_refine on Sun Mar 10 14:51:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/03_2024/7t2e_25611.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/03_2024/7t2e_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_25611/03_2024/7t2e_25611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/03_2024/7t2e_25611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/03_2024/7t2e_25611.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2e_25611/03_2024/7t2e_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 1.72, per 1000 atoms: 0.72 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: 0.83 Conformation dependent library (CDL) restraints added in 439.5 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: 0.25 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: 0.55 Time building geometry restraints manager: 0.93 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: 0.740 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: 3.420 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.310 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.830 ------------------------------------------------------------------------------- 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 : 0.265 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 1.4582 time to fit residues: 55.0891 Evaluate side-chains 38 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain B residue 63 GLU 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: 0.0460 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= 0.199 Angle : 0.501 4.239 3342 Z= 0.263 Chirality : 0.046 0.146 364 Planarity : 0.004 0.029 434 Dihedral : 5.330 45.351 339 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.36 % Allowed : 22.44 % 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: 0.44 (0.47), residues: 308 helix: 2.36 (1.09), residues: 28 sheet: -0.06 (0.40), residues: 158 loop : 0.53 (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 50 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.250 Fit side-chains REVERT: A 31 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8196 (mm) outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 1.2309 time to fit residues: 59.1580 Evaluate side-chains 38 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 109 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2450 Z= 0.357 Angle : 0.594 5.043 3342 Z= 0.312 Chirality : 0.049 0.155 364 Planarity : 0.004 0.037 434 Dihedral : 4.684 18.119 334 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.71 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: 0.15 (0.47), residues: 308 helix: 1.90 (1.06), residues: 28 sheet: -0.17 (0.40), residues: 158 loop : 0.28 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 18 PHE 0.018 0.003 PHE A 120 TYR 0.008 0.001 TYR A 108 ARG 0.003 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 42 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.270 Fit side-chains REVERT: A 31 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8248 (mm) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 1.3414 time to fit residues: 53.3764 Evaluate side-chains 42 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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: 0.8198 moved from start: 0.0761 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= 0.195 Angle : 0.492 4.176 3342 Z= 0.258 Chirality : 0.046 0.144 364 Planarity : 0.004 0.033 434 Dihedral : 4.208 16.455 334 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 : 2.76 % Allowed : 22.44 % 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: 0.28 (0.47), residues: 308 helix: 2.17 (1.04), residues: 28 sheet: -0.13 (0.40), residues: 158 loop : 0.41 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 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 50 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.290 Fit side-chains REVERT: A 31 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8223 (mm) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 1.2545 time to fit residues: 58.9941 Evaluate side-chains 48 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 63 GLU 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: 0.6980 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.8198 moved from start: 0.0822 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= 0.194 Angle : 0.489 4.188 3342 Z= 0.256 Chirality : 0.046 0.145 364 Planarity : 0.003 0.032 434 Dihedral : 4.132 16.358 334 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.54 % Allowed : 22.05 % 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: 0.31 (0.47), residues: 308 helix: 2.19 (1.03), residues: 28 sheet: -0.13 (0.40), residues: 158 loop : 0.45 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 PHE 0.012 0.002 PHE A 120 TYR 0.008 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 50 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.283 Fit side-chains REVERT: A 31 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8235 (mm) outliers start: 9 outliers final: 7 residues processed: 46 average time/residue: 1.2531 time to fit residues: 58.9348 Evaluate side-chains 43 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 63 GLU 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: 0.0770 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2450 Z= 0.287 Angle : 0.547 4.518 3342 Z= 0.286 Chirality : 0.047 0.149 364 Planarity : 0.004 0.037 434 Dihedral : 4.419 17.783 334 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.15 % Allowed : 22.05 % 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: 0.18 (0.47), residues: 308 helix: 1.98 (1.04), residues: 28 sheet: -0.16 (0.40), residues: 158 loop : 0.32 (0.53), 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 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 42 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.243 Fit side-chains REVERT: A 31 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8249 (mm) outliers start: 8 outliers final: 7 residues processed: 39 average time/residue: 1.4195 time to fit residues: 56.5299 Evaluate side-chains 42 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 63 GLU 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: 4.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.0835 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= 0.180 Angle : 0.480 4.219 3342 Z= 0.251 Chirality : 0.045 0.145 364 Planarity : 0.003 0.034 434 Dihedral : 4.080 16.111 334 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 22.83 % 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: 0.31 (0.47), residues: 308 helix: 2.17 (1.02), residues: 28 sheet: -0.13 (0.40), residues: 158 loop : 0.45 (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 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 43 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.293 Fit side-chains REVERT: A 31 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8229 (mm) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 1.3367 time to fit residues: 53.2925 Evaluate side-chains 42 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU 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: 4.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.0849 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= 0.183 Angle : 0.482 4.285 3342 Z= 0.251 Chirality : 0.045 0.145 364 Planarity : 0.003 0.034 434 Dihedral : 4.058 16.045 334 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.15 % Allowed : 22.44 % 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: 0.34 (0.47), residues: 308 helix: 2.16 (1.02), residues: 28 sheet: -0.11 (0.40), residues: 158 loop : 0.49 (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 0.008 0.001 TYR A 108 ARG 0.001 0.000 ARG A 155 *********************** 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 43 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.278 Fit side-chains REVERT: A 31 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8222 (mm) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 1.3976 time to fit residues: 55.6541 Evaluate side-chains 42 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2450 Z= 0.285 Angle : 0.541 4.505 3342 Z= 0.283 Chirality : 0.047 0.151 364 Planarity : 0.004 0.038 434 Dihedral : 4.387 17.743 334 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.15 % Allowed : 22.44 % 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: 0.21 (0.47), residues: 308 helix: 2.06 (1.03), residues: 28 sheet: -0.15 (0.40), residues: 158 loop : 0.33 (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 41 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.281 Fit side-chains REVERT: A 31 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8262 (mm) outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 1.4939 time to fit residues: 56.4502 Evaluate side-chains 40 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU 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: 5.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2450 Z= 0.328 Angle : 0.567 4.774 3342 Z= 0.296 Chirality : 0.048 0.152 364 Planarity : 0.004 0.040 434 Dihedral : 4.512 18.184 334 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 22.83 % 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: 0.11 (0.47), residues: 308 helix: 1.95 (1.03), residues: 28 sheet: -0.19 (0.40), residues: 158 loop : 0.25 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 18 PHE 0.017 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 40 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.287 Fit side-chains REVERT: A 31 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8270 (mm) outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 1.4656 time to fit residues: 55.4060 Evaluate side-chains 40 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.113102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.091645 restraints weight = 2935.883| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.14 r_work: 0.2932 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0904 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= 0.125 Angle : 0.447 4.211 3342 Z= 0.233 Chirality : 0.044 0.141 364 Planarity : 0.003 0.035 434 Dihedral : 3.828 14.337 334 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.36 % Allowed : 23.23 % 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: 0.37 (0.47), residues: 308 helix: 2.33 (1.02), residues: 28 sheet: -0.12 (0.40), residues: 158 loop : 0.52 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 123 PHE 0.010 0.002 PHE B 120 TYR 0.007 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: 1481.11 seconds wall clock time: 26 minutes 59.47 seconds (1619.47 seconds total)