Starting phenix.real_space_refine on Thu Dec 7 23:26:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/12_2023/7vag_31840.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/12_2023/7vag_31840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/12_2023/7vag_31840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/12_2023/7vag_31840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/12_2023/7vag_31840.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/12_2023/7vag_31840.pdb" } resolution = 3.32 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= 0.003 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 43 5.16 5 C 3676 2.51 5 N 912 2.21 5 O 1066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H ASP 102": "OD1" <-> "OD2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 128": "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: 5697 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2344 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1669 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 15, 'TRANS': 205} Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Time building chain proxies: 3.67, per 1000 atoms: 0.64 Number of scatterers: 5697 At special positions: 0 Unit cell: (84.66, 72.21, 140.685, 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 43 16.00 O 1066 8.00 N 912 7.00 C 3676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 38.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.661A pdb=" N GLY A 19 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 45 removed outlier: 4.106A pdb=" N THR A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.617A pdb=" N ILE A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.840A pdb=" N ILE A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.698A pdb=" N ASN A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 209 removed outlier: 3.510A pdb=" N VAL A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix removed outlier: 3.526A pdb=" N PHE A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.528A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.793A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.743A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY H 66 " --> pdb=" O LYS H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 66' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.866A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.952A pdb=" N LEU L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.514A pdb=" N LEU L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.606A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.028A pdb=" N CYS H 96 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TYR H 110 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG H 98 " --> pdb=" O PHE H 108 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR H 100 " --> pdb=" O HIS H 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 130 through 132 removed outlier: 4.340A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER H 187 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 161 removed outlier: 3.644A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.527A pdb=" N TYR L 92 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 21 through 23 removed outlier: 3.673A pdb=" N CYS L 23 " --> pdb=" O PHE L 77 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE L 77 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 122 through 123 removed outlier: 3.574A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 158 through 159 283 hydrogen bonds defined for protein. 753 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: 1.58 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1734 1.35 - 1.46: 1443 1.46 - 1.58: 2593 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 5835 Sorted by residual: bond pdb=" CA MET A 133 " pdb=" CB MET A 133 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.84e-02 2.95e+03 1.08e+00 bond pdb=" CB GLN H 179 " pdb=" CG GLN H 179 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.00e+00 bond pdb=" CA GLN H 179 " pdb=" CB GLN H 179 " ideal model delta sigma weight residual 1.533 1.549 -0.016 1.69e-02 3.50e+03 8.61e-01 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.57e-01 bond pdb=" CB MET A 256 " pdb=" CG MET A 256 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.25e-01 ... (remaining 5830 not shown) Histogram of bond angle deviations from ideal: 97.39 - 104.72: 115 104.72 - 112.05: 2970 112.05 - 119.38: 1801 119.38 - 126.71: 2956 126.71 - 134.04: 87 Bond angle restraints: 7929 Sorted by residual: angle pdb=" CA GLN H 179 " pdb=" CB GLN H 179 " pdb=" CG GLN H 179 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.09e+00 angle pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " pdb=" CG LEU A 150 " ideal model delta sigma weight residual 116.30 125.69 -9.39 3.50e+00 8.16e-02 7.20e+00 angle pdb=" CB MET A 133 " pdb=" CG MET A 133 " pdb=" SD MET A 133 " ideal model delta sigma weight residual 112.70 120.74 -8.04 3.00e+00 1.11e-01 7.19e+00 angle pdb=" N MET A 133 " pdb=" CA MET A 133 " pdb=" CB MET A 133 " ideal model delta sigma weight residual 111.66 107.78 3.88 1.56e+00 4.11e-01 6.18e+00 angle pdb=" CB MET A 39 " pdb=" CG MET A 39 " pdb=" SD MET A 39 " ideal model delta sigma weight residual 112.70 119.71 -7.01 3.00e+00 1.11e-01 5.45e+00 ... (remaining 7924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3179 17.95 - 35.90: 258 35.90 - 53.85: 33 53.85 - 71.80: 7 71.80 - 89.75: 4 Dihedral angle restraints: 3481 sinusoidal: 1329 harmonic: 2152 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 165.03 -72.03 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB GLU L 192 " pdb=" CG GLU L 192 " pdb=" CD GLU L 192 " pdb=" OE1 GLU L 192 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA GLY A 132 " pdb=" C GLY A 132 " pdb=" N MET A 133 " pdb=" CA MET A 133 " ideal model delta harmonic sigma weight residual 180.00 -164.19 -15.81 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 3478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 550 0.029 - 0.058: 230 0.058 - 0.088: 80 0.088 - 0.117: 52 0.117 - 0.146: 6 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE H 104 " pdb=" N ILE H 104 " pdb=" C ILE H 104 " pdb=" CB ILE H 104 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CG LEU A 118 " pdb=" CB LEU A 118 " pdb=" CD1 LEU A 118 " pdb=" CD2 LEU A 118 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CB ILE A 214 " pdb=" CA ILE A 214 " pdb=" CG1 ILE A 214 " pdb=" CG2 ILE A 214 " both_signs ideal model delta sigma weight residual False 2.64 2.77 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 915 not shown) Planarity restraints: 980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR H 213 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.78e+00 pdb=" C THR H 213 " 0.023 2.00e-02 2.50e+03 pdb=" O THR H 213 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL H 214 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 174 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO H 175 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO H 175 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 175 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 280 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 281 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.015 5.00e-02 4.00e+02 ... (remaining 977 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 77 2.67 - 3.23: 5522 3.23 - 3.78: 8655 3.78 - 4.34: 11118 4.34 - 4.90: 18741 Nonbonded interactions: 44113 Sorted by model distance: nonbonded pdb=" OG SER H 198 " pdb=" OE1 GLN H 199 " model vdw 2.109 2.440 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 115 " model vdw 2.239 2.440 nonbonded pdb=" OH TYR A 69 " pdb=" O SER A 126 " model vdw 2.293 2.440 nonbonded pdb=" OE2 GLU A 47 " pdb=" NZ LYS A 50 " model vdw 2.295 2.520 nonbonded pdb=" NH2 ARG L 60 " pdb=" O VAL L 64 " model vdw 2.317 2.520 ... (remaining 44108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.940 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5835 Z= 0.150 Angle : 0.655 9.395 7929 Z= 0.311 Chirality : 0.041 0.146 918 Planarity : 0.004 0.031 980 Dihedral : 13.266 89.754 2096 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.15 % Allowed : 0.77 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.32), residues: 737 helix: 1.46 (0.33), residues: 250 sheet: 0.88 (0.41), residues: 168 loop : -1.04 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 56 HIS 0.002 0.000 HIS H 35 PHE 0.014 0.001 PHE A 292 TYR 0.010 0.001 TYR A 146 ARG 0.005 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1556 time to fit residues: 44.1535 Evaluate side-chains 186 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 293 GLN H 39 GLN H 113 GLN H 179 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 195 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5835 Z= 0.374 Angle : 0.766 10.436 7929 Z= 0.377 Chirality : 0.047 0.186 918 Planarity : 0.005 0.043 980 Dihedral : 4.443 18.403 794 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.79 % Allowed : 15.02 % Favored : 82.20 % 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: 0.16 (0.31), residues: 737 helix: 1.39 (0.33), residues: 253 sheet: 0.59 (0.40), residues: 170 loop : -1.26 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 196 HIS 0.006 0.002 HIS H 207 PHE 0.029 0.003 PHE A 274 TYR 0.023 0.002 TYR A 146 ARG 0.003 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 202 time to evaluate : 0.652 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 207 average time/residue: 0.1490 time to fit residues: 41.2486 Evaluate side-chains 203 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0924 time to fit residues: 2.4877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.0470 chunk 20 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5835 Z= 0.191 Angle : 0.688 11.048 7929 Z= 0.329 Chirality : 0.044 0.199 918 Planarity : 0.004 0.038 980 Dihedral : 4.323 17.521 794 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.63 % Allowed : 18.42 % Favored : 78.95 % 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: 0.36 (0.32), residues: 737 helix: 1.71 (0.34), residues: 253 sheet: 0.68 (0.40), residues: 168 loop : -1.27 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 153 HIS 0.003 0.001 HIS H 207 PHE 0.022 0.001 PHE A 274 TYR 0.020 0.001 TYR H 153 ARG 0.003 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 0.676 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 206 average time/residue: 0.1514 time to fit residues: 41.8056 Evaluate side-chains 197 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0580 time to fit residues: 1.8003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 293 GLN H 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5835 Z= 0.194 Angle : 0.691 11.251 7929 Z= 0.328 Chirality : 0.043 0.207 918 Planarity : 0.004 0.035 980 Dihedral : 4.302 17.477 794 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.79 % Allowed : 21.36 % Favored : 75.85 % 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 (0.32), residues: 737 helix: 1.78 (0.34), residues: 254 sheet: 0.52 (0.40), residues: 169 loop : -1.29 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 168 HIS 0.003 0.001 HIS H 207 PHE 0.021 0.001 PHE A 292 TYR 0.015 0.001 TYR H 153 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 193 time to evaluate : 0.639 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 194 average time/residue: 0.1440 time to fit residues: 37.4903 Evaluate side-chains 194 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 184 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0572 time to fit residues: 1.9061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN H 179 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5835 Z= 0.218 Angle : 0.704 8.310 7929 Z= 0.335 Chirality : 0.044 0.206 918 Planarity : 0.004 0.036 980 Dihedral : 4.336 18.346 794 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.79 % Allowed : 22.14 % Favored : 75.08 % 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 (0.32), residues: 737 helix: 1.82 (0.34), residues: 254 sheet: 0.50 (0.41), residues: 169 loop : -1.35 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 207 PHE 0.022 0.002 PHE A 292 TYR 0.018 0.001 TYR L 145 ARG 0.003 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 0.682 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 201 average time/residue: 0.1522 time to fit residues: 41.2914 Evaluate side-chains 197 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 188 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0609 time to fit residues: 1.8548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 0.0270 chunk 32 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 293 GLN H 39 GLN H 179 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5835 Z= 0.178 Angle : 0.698 9.631 7929 Z= 0.329 Chirality : 0.043 0.205 918 Planarity : 0.004 0.035 980 Dihedral : 4.264 18.600 794 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.08 % Allowed : 23.37 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.32), residues: 737 helix: 2.02 (0.35), residues: 241 sheet: 0.66 (0.41), residues: 162 loop : -1.32 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 168 HIS 0.002 0.001 HIS H 35 PHE 0.019 0.001 PHE A 292 TYR 0.014 0.001 TYR H 153 ARG 0.005 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 190 time to evaluate : 0.656 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 192 average time/residue: 0.1472 time to fit residues: 38.4400 Evaluate side-chains 186 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0659 time to fit residues: 1.2702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 293 GLN H 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5835 Z= 0.218 Angle : 0.713 9.096 7929 Z= 0.337 Chirality : 0.045 0.214 918 Planarity : 0.004 0.037 980 Dihedral : 4.313 19.418 794 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 1.39 % Allowed : 24.61 % Favored : 73.99 % 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: 0.27 (0.32), residues: 737 helix: 1.92 (0.35), residues: 242 sheet: 0.46 (0.40), residues: 169 loop : -1.36 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.023 0.001 PHE A 292 TYR 0.014 0.001 TYR L 145 ARG 0.004 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 191 time to evaluate : 0.635 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 193 average time/residue: 0.1529 time to fit residues: 40.0776 Evaluate side-chains 192 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 0.644 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0641 time to fit residues: 1.5632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.0470 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 293 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5835 Z= 0.176 Angle : 0.705 9.132 7929 Z= 0.332 Chirality : 0.043 0.216 918 Planarity : 0.004 0.033 980 Dihedral : 4.249 18.937 794 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.08 % Allowed : 24.77 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.32), residues: 737 helix: 1.87 (0.34), residues: 242 sheet: 0.62 (0.41), residues: 162 loop : -1.35 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 168 HIS 0.002 0.001 HIS H 35 PHE 0.019 0.001 PHE A 292 TYR 0.016 0.001 TYR H 153 ARG 0.010 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 0.664 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 191 average time/residue: 0.1478 time to fit residues: 38.0496 Evaluate side-chains 186 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0540 time to fit residues: 1.2192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 293 GLN H 179 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5835 Z= 0.263 Angle : 0.752 11.060 7929 Z= 0.359 Chirality : 0.046 0.211 918 Planarity : 0.004 0.038 980 Dihedral : 4.512 20.009 794 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 1.24 % Allowed : 24.92 % Favored : 73.84 % 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: 0.09 (0.32), residues: 737 helix: 1.75 (0.35), residues: 240 sheet: 0.36 (0.40), residues: 169 loop : -1.43 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 168 HIS 0.004 0.001 HIS H 207 PHE 0.032 0.002 PHE A 292 TYR 0.015 0.002 TYR H 95 ARG 0.007 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 195 average time/residue: 0.1498 time to fit residues: 39.0306 Evaluate side-chains 195 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1550 time to fit residues: 1.8936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 271 ASN A 293 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5835 Z= 0.214 Angle : 0.767 13.377 7929 Z= 0.357 Chirality : 0.045 0.236 918 Planarity : 0.004 0.037 980 Dihedral : 4.435 19.742 794 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.15 % Allowed : 26.47 % Favored : 73.37 % 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: 0.05 (0.32), residues: 737 helix: 1.67 (0.35), residues: 241 sheet: 0.21 (0.40), residues: 179 loop : -1.40 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.027 0.001 PHE A 292 TYR 0.015 0.001 TYR H 95 ARG 0.011 0.001 ARG A 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 186 average time/residue: 0.1529 time to fit residues: 37.9545 Evaluate side-chains 186 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0551 time to fit residues: 1.0031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 293 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121350 restraints weight = 9478.232| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.51 r_work: 0.3326 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5835 Z= 0.207 Angle : 0.738 10.920 7929 Z= 0.346 Chirality : 0.045 0.218 918 Planarity : 0.004 0.037 980 Dihedral : 4.369 19.803 794 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.15 % Allowed : 26.93 % Favored : 72.91 % 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: -0.04 (0.32), residues: 737 helix: 1.57 (0.35), residues: 241 sheet: 0.36 (0.40), residues: 169 loop : -1.51 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.028 0.001 PHE A 292 TYR 0.015 0.001 TYR H 95 ARG 0.010 0.001 ARG A 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1667.44 seconds wall clock time: 30 minutes 54.96 seconds (1854.96 seconds total)