Starting phenix.real_space_refine on Sun Mar 10 22:38:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/03_2024/7vag_31840.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/03_2024/7vag_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_31840/03_2024/7vag_31840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/03_2024/7vag_31840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/03_2024/7vag_31840.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vag_31840/03_2024/7vag_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-dev-5265/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: 3.68, per 1000 atoms: 0.65 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: 2.21 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: 1.57 Time building geometry restraints manager: 2.40 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: 0.520 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: 2.060 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.920 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.600 ------------------------------------------------------------------------------- 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 : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7666 (ttm-80) REVERT: A 229 MET cc_start: 0.8523 (tpt) cc_final: 0.8039 (tpt) REVERT: A 308 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7435 (tp30) REVERT: H 91 SER cc_start: 0.8947 (m) cc_final: 0.8706 (p) REVERT: H 153 TYR cc_start: 0.6429 (p90) cc_final: 0.5833 (p90) REVERT: L 144 PHE cc_start: 0.8461 (p90) cc_final: 0.8190 (p90) REVERT: L 180 MET cc_start: 0.8413 (ttp) cc_final: 0.8086 (ttt) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1568 time to fit residues: 44.5078 Evaluate side-chains 185 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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: 0.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5835 Z= 0.403 Angle : 0.800 10.432 7929 Z= 0.397 Chirality : 0.049 0.189 918 Planarity : 0.005 0.045 980 Dihedral : 4.697 19.451 794 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.25 % Allowed : 16.10 % Favored : 80.65 % 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: -0.02 (0.31), residues: 737 helix: 1.19 (0.32), residues: 254 sheet: 0.58 (0.41), residues: 164 loop : -1.35 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 196 HIS 0.008 0.002 HIS L 194 PHE 0.027 0.003 PHE A 292 TYR 0.022 0.002 TYR A 146 ARG 0.004 0.001 ARG L 193 *********************** 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 225 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.5533 (mmp) cc_final: 0.5140 (mmt) REVERT: A 229 MET cc_start: 0.8725 (tpt) cc_final: 0.8240 (tpt) REVERT: A 271 ASN cc_start: 0.8862 (m-40) cc_final: 0.8626 (m110) REVERT: H 91 SER cc_start: 0.8895 (m) cc_final: 0.8606 (p) REVERT: H 153 TYR cc_start: 0.6858 (p90) cc_final: 0.6027 (p90) REVERT: H 179 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7246 (pp30) REVERT: L 4 MET cc_start: 0.8433 (mmm) cc_final: 0.7524 (mmm) REVERT: L 144 PHE cc_start: 0.8513 (p90) cc_final: 0.8103 (p90) outliers start: 21 outliers final: 15 residues processed: 209 average time/residue: 0.1470 time to fit residues: 41.1785 Evaluate side-chains 208 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 18 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2784 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= 0.271 Angle : 0.720 12.021 7929 Z= 0.347 Chirality : 0.045 0.206 918 Planarity : 0.004 0.044 980 Dihedral : 4.599 18.780 794 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.18 % Allowed : 21.21 % Favored : 74.61 % 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 (0.31), residues: 737 helix: 1.57 (0.34), residues: 254 sheet: 0.47 (0.40), residues: 169 loop : -1.38 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.003 0.001 HIS H 207 PHE 0.027 0.002 PHE A 292 TYR 0.017 0.002 TYR A 146 ARG 0.003 0.000 ARG A 249 *********************** 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 223 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 0.644 Fit side-chains REVERT: A 184 MET cc_start: 0.5566 (mmp) cc_final: 0.5238 (mmt) REVERT: A 229 MET cc_start: 0.8663 (tpt) cc_final: 0.8236 (tpt) REVERT: H 153 TYR cc_start: 0.7108 (p90) cc_final: 0.6258 (p90) REVERT: L 4 MET cc_start: 0.8394 (mmm) cc_final: 0.7658 (mmm) REVERT: L 144 PHE cc_start: 0.8502 (p90) cc_final: 0.8135 (p90) outliers start: 27 outliers final: 18 residues processed: 207 average time/residue: 0.1468 time to fit residues: 40.8308 Evaluate side-chains 208 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 194 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5835 Z= 0.274 Angle : 0.721 10.017 7929 Z= 0.346 Chirality : 0.045 0.203 918 Planarity : 0.004 0.043 980 Dihedral : 4.609 19.694 794 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.49 % Allowed : 21.83 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.31), residues: 737 helix: 1.75 (0.35), residues: 247 sheet: 0.35 (0.40), residues: 168 loop : -1.47 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 168 HIS 0.004 0.001 HIS H 207 PHE 0.030 0.002 PHE A 292 TYR 0.017 0.002 TYR A 146 ARG 0.002 0.000 ARG A 249 *********************** 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 225 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 0.679 Fit side-chains REVERT: A 184 MET cc_start: 0.5444 (mmp) cc_final: 0.5131 (mmt) REVERT: A 229 MET cc_start: 0.8792 (tpt) cc_final: 0.8352 (tpt) REVERT: H 153 TYR cc_start: 0.7257 (p90) cc_final: 0.6412 (p90) REVERT: L 4 MET cc_start: 0.8424 (mmm) cc_final: 0.7771 (mmm) REVERT: L 144 PHE cc_start: 0.8521 (p90) cc_final: 0.8085 (p90) REVERT: L 161 GLN cc_start: 0.5625 (mp10) cc_final: 0.5119 (mp10) outliers start: 29 outliers final: 23 residues processed: 204 average time/residue: 0.1436 time to fit residues: 39.6979 Evaluate side-chains 212 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 194 HIS 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: 1.9990 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3315 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= 0.224 Angle : 0.710 9.139 7929 Z= 0.336 Chirality : 0.044 0.194 918 Planarity : 0.004 0.039 980 Dihedral : 4.491 19.635 794 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 5.26 % Allowed : 22.91 % Favored : 71.83 % 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: 0.10 (0.32), residues: 737 helix: 1.81 (0.34), residues: 248 sheet: 0.16 (0.40), residues: 169 loop : -1.43 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 56 HIS 0.003 0.001 HIS H 35 PHE 0.023 0.002 PHE A 292 TYR 0.016 0.001 TYR A 139 ARG 0.002 0.000 ARG A 249 *********************** 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 232 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 192 MET cc_start: 0.5891 (mtm) cc_final: 0.5622 (mtp) REVERT: A 271 ASN cc_start: 0.8787 (m-40) cc_final: 0.8569 (m110) REVERT: A 294 LEU cc_start: 0.9073 (tt) cc_final: 0.8717 (tt) REVERT: H 100 TYR cc_start: 0.8374 (t80) cc_final: 0.8155 (t80) REVERT: H 153 TYR cc_start: 0.7083 (p90) cc_final: 0.6302 (p90) REVERT: L 4 MET cc_start: 0.8411 (mmm) cc_final: 0.7766 (mmm) REVERT: L 144 PHE cc_start: 0.8476 (p90) cc_final: 0.8112 (p90) outliers start: 34 outliers final: 27 residues processed: 210 average time/residue: 0.1458 time to fit residues: 41.3542 Evaluate side-chains 218 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 194 HIS Chi-restraints excluded: chain L residue 215 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 43 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: 0.7791 moved from start: 0.3496 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= 0.228 Angle : 0.712 8.754 7929 Z= 0.339 Chirality : 0.044 0.190 918 Planarity : 0.004 0.039 980 Dihedral : 4.485 20.041 794 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.80 % Allowed : 24.46 % Favored : 70.74 % 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: 1.81 (0.34), residues: 247 sheet: 0.14 (0.41), residues: 165 loop : -1.41 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 56 HIS 0.003 0.001 HIS H 35 PHE 0.024 0.001 PHE A 292 TYR 0.016 0.001 TYR H 95 ARG 0.003 0.000 ARG A 251 *********************** 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 229 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 198 time to evaluate : 0.664 Fit side-chains REVERT: A 192 MET cc_start: 0.5945 (mtm) cc_final: 0.5661 (mtp) REVERT: A 294 LEU cc_start: 0.9054 (tt) cc_final: 0.8707 (tt) REVERT: H 100 TYR cc_start: 0.8375 (t80) cc_final: 0.8156 (t80) REVERT: H 153 TYR cc_start: 0.7156 (p90) cc_final: 0.6295 (p90) REVERT: L 4 MET cc_start: 0.8333 (mmm) cc_final: 0.7788 (mmm) REVERT: L 144 PHE cc_start: 0.8480 (p90) cc_final: 0.8178 (p90) outliers start: 31 outliers final: 27 residues processed: 208 average time/residue: 0.1510 time to fit residues: 42.4241 Evaluate side-chains 221 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 194 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 161 GLN ** 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: 0.7773 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5835 Z= 0.195 Angle : 0.725 9.570 7929 Z= 0.340 Chirality : 0.043 0.192 918 Planarity : 0.004 0.038 980 Dihedral : 4.412 19.853 794 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.33 % Allowed : 26.01 % Favored : 69.66 % 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: 0.02 (0.32), residues: 737 helix: 1.69 (0.34), residues: 246 sheet: 0.16 (0.41), residues: 162 loop : -1.40 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 56 HIS 0.002 0.001 HIS H 35 PHE 0.019 0.001 PHE A 292 TYR 0.013 0.001 TYR H 95 ARG 0.010 0.000 ARG A 249 *********************** 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 225 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8803 (m-10) cc_final: 0.8563 (m-10) REVERT: A 127 THR cc_start: 0.9023 (m) cc_final: 0.8789 (p) REVERT: A 163 LEU cc_start: 0.9036 (tp) cc_final: 0.8706 (mp) REVERT: A 271 ASN cc_start: 0.8790 (m-40) cc_final: 0.8581 (m110) REVERT: A 294 LEU cc_start: 0.9012 (tt) cc_final: 0.8780 (tt) REVERT: H 100 TYR cc_start: 0.8353 (t80) cc_final: 0.8153 (t80) REVERT: H 153 TYR cc_start: 0.7116 (p90) cc_final: 0.6312 (p90) REVERT: L 4 MET cc_start: 0.8327 (mmm) cc_final: 0.7753 (mmm) REVERT: L 144 PHE cc_start: 0.8436 (p90) cc_final: 0.8190 (p90) REVERT: L 161 GLN cc_start: 0.5777 (mp10) cc_final: 0.5550 (mp10) outliers start: 28 outliers final: 24 residues processed: 206 average time/residue: 0.1493 time to fit residues: 41.4121 Evaluate side-chains 214 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 194 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7784 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5835 Z= 0.217 Angle : 0.732 10.179 7929 Z= 0.345 Chirality : 0.044 0.192 918 Planarity : 0.004 0.037 980 Dihedral : 4.415 19.951 794 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.33 % Allowed : 26.32 % Favored : 69.35 % 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: -0.03 (0.32), residues: 737 helix: 1.68 (0.34), residues: 246 sheet: -0.02 (0.40), residues: 169 loop : -1.39 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 56 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.001 PHE A 292 TYR 0.020 0.001 TYR A 139 ARG 0.007 0.000 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 222 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8802 (m-40) cc_final: 0.8592 (m110) REVERT: A 294 LEU cc_start: 0.9003 (tt) cc_final: 0.8673 (tt) REVERT: H 153 TYR cc_start: 0.7206 (p90) cc_final: 0.6329 (p90) REVERT: L 4 MET cc_start: 0.8338 (mmm) cc_final: 0.7797 (mmm) REVERT: L 144 PHE cc_start: 0.8449 (p90) cc_final: 0.8204 (p90) REVERT: L 161 GLN cc_start: 0.5923 (mp10) cc_final: 0.5658 (mp10) outliers start: 28 outliers final: 26 residues processed: 204 average time/residue: 0.1495 time to fit residues: 40.9197 Evaluate side-chains 218 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 194 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3682 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= 0.212 Angle : 0.737 10.567 7929 Z= 0.346 Chirality : 0.044 0.197 918 Planarity : 0.004 0.039 980 Dihedral : 4.406 20.437 794 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.49 % Allowed : 26.47 % Favored : 69.04 % 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: -0.03 (0.32), residues: 737 helix: 1.64 (0.34), residues: 246 sheet: -0.06 (0.41), residues: 172 loop : -1.34 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 56 HIS 0.002 0.001 HIS H 35 PHE 0.023 0.001 PHE A 292 TYR 0.020 0.001 TYR A 139 ARG 0.008 0.000 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 223 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 228 LEU cc_start: 0.9087 (tp) cc_final: 0.8753 (tt) REVERT: A 271 ASN cc_start: 0.8800 (m-40) cc_final: 0.8589 (m110) REVERT: A 294 LEU cc_start: 0.8996 (tt) cc_final: 0.8680 (tt) REVERT: A 310 PHE cc_start: 0.6385 (m-80) cc_final: 0.6156 (m-80) REVERT: H 153 TYR cc_start: 0.7236 (p90) cc_final: 0.6314 (p90) REVERT: L 4 MET cc_start: 0.8342 (mmm) cc_final: 0.7795 (mmm) REVERT: L 161 GLN cc_start: 0.6027 (mp10) cc_final: 0.5415 (mp10) REVERT: L 179 SER cc_start: 0.8883 (m) cc_final: 0.8345 (m) outliers start: 29 outliers final: 26 residues processed: 204 average time/residue: 0.1502 time to fit residues: 40.9425 Evaluate side-chains 222 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 194 HIS Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.0070 chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5835 Z= 0.190 Angle : 0.741 9.515 7929 Z= 0.346 Chirality : 0.044 0.194 918 Planarity : 0.004 0.038 980 Dihedral : 4.274 20.186 794 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.02 % Allowed : 27.55 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.32), residues: 737 helix: 1.61 (0.34), residues: 247 sheet: 0.17 (0.42), residues: 162 loop : -1.42 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 56 HIS 0.002 0.001 HIS H 35 PHE 0.022 0.001 PHE A 292 TYR 0.017 0.001 TYR A 139 ARG 0.007 0.000 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 225 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.8972 (tp) cc_final: 0.8700 (tt) REVERT: A 271 ASN cc_start: 0.8750 (m-40) cc_final: 0.8537 (m110) REVERT: H 153 TYR cc_start: 0.7165 (p90) cc_final: 0.6241 (p90) REVERT: L 4 MET cc_start: 0.8438 (mmm) cc_final: 0.7789 (mmm) REVERT: L 161 GLN cc_start: 0.6129 (mp10) cc_final: 0.5544 (mp10) REVERT: L 179 SER cc_start: 0.8774 (m) cc_final: 0.8482 (m) outliers start: 26 outliers final: 25 residues processed: 208 average time/residue: 0.1511 time to fit residues: 41.9408 Evaluate side-chains 213 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 194 HIS Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122560 restraints weight = 9244.336| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.52 r_work: 0.3338 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3786 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= 0.195 Angle : 0.754 9.558 7929 Z= 0.348 Chirality : 0.044 0.184 918 Planarity : 0.004 0.041 980 Dihedral : 4.251 20.095 794 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.18 % Allowed : 27.71 % Favored : 68.11 % 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: 1.62 (0.35), residues: 247 sheet: 0.14 (0.42), residues: 163 loop : -1.45 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 56 HIS 0.002 0.001 HIS H 35 PHE 0.018 0.001 PHE A 292 TYR 0.019 0.001 TYR A 139 ARG 0.007 0.000 ARG A 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.66 seconds wall clock time: 31 minutes 16.35 seconds (1876.35 seconds total)