Starting phenix.real_space_refine on Fri Jul 19 00:53:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/07_2024/8p76_17519.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/07_2024/8p76_17519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/07_2024/8p76_17519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/07_2024/8p76_17519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/07_2024/8p76_17519.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/07_2024/8p76_17519.cif" } resolution = 2.0 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= 0.001 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 31 5.16 5 C 3296 2.51 5 N 870 2.21 5 O 1064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ASP 299": "OD1" <-> "OD2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I GLU 229": "OE1" <-> "OE2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J GLU 147": "OE1" <-> "OE2" Residue "J TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J GLU 235": "OE1" <-> "OE2" Residue "J TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 270": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5261 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'X1W': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Time building chain proxies: 4.42, per 1000 atoms: 0.84 Number of scatterers: 5261 At special positions: 0 Unit cell: (84.7875, 93.3375, 68.4, 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 31 16.00 O 1064 8.00 N 870 7.00 C 3296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 62.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'H' and resid 262 through 275 removed outlier: 4.474A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY H 270 " --> pdb=" O GLY H 267 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR H 271 " --> pdb=" O ARG H 268 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU H 272 " --> pdb=" O LEU H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.872A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 36 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.899A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 117 Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.706A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 188 through 201 removed outlier: 3.640A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.502A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 283 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.877A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20 removed outlier: 6.042A pdb=" N LYS J 14 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG J 30 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 279 hydrogen bonds defined for protein. 765 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: 1.37 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1642 1.34 - 1.46: 1183 1.46 - 1.58: 2358 1.58 - 1.70: 3 1.70 - 1.82: 49 Bond restraints: 5235 Sorted by residual: bond pdb=" C08 X1W J 401 " pdb=" N09 X1W J 401 " ideal model delta sigma weight residual 1.337 1.490 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C26 X1W J 401 " pdb=" C27 X1W J 401 " ideal model delta sigma weight residual 1.502 1.610 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C02 X1W J 401 " pdb=" C04 X1W J 401 " ideal model delta sigma weight residual 1.498 1.600 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C18 X1W J 401 " pdb=" N19 X1W J 401 " ideal model delta sigma weight residual 1.356 1.454 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C20 X1W J 401 " pdb=" C24 X1W J 401 " ideal model delta sigma weight residual 1.528 1.621 -0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 5230 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.68: 136 105.68 - 112.74: 2729 112.74 - 119.80: 1744 119.80 - 126.86: 2402 126.86 - 133.92: 74 Bond angle restraints: 7085 Sorted by residual: angle pdb=" CG ARG I 279 " pdb=" CD ARG I 279 " pdb=" NE ARG I 279 " ideal model delta sigma weight residual 112.00 118.65 -6.65 2.20e+00 2.07e-01 9.15e+00 angle pdb=" CA MET I 237 " pdb=" CB MET I 237 " pdb=" CG MET I 237 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-01 8.42e+00 angle pdb=" CB MET I 237 " pdb=" CG MET I 237 " pdb=" SD MET I 237 " ideal model delta sigma weight residual 112.70 120.84 -8.14 3.00e+00 1.11e-01 7.35e+00 angle pdb=" CB MET J 94 " pdb=" CG MET J 94 " pdb=" SD MET J 94 " ideal model delta sigma weight residual 112.70 120.06 -7.36 3.00e+00 1.11e-01 6.01e+00 angle pdb=" CA GLU I 137 " pdb=" CB GLU I 137 " pdb=" CG GLU I 137 " ideal model delta sigma weight residual 114.10 118.98 -4.88 2.00e+00 2.50e-01 5.96e+00 ... (remaining 7080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 2751 17.71 - 35.43: 317 35.43 - 53.14: 72 53.14 - 70.86: 23 70.86 - 88.57: 8 Dihedral angle restraints: 3171 sinusoidal: 1324 harmonic: 1847 Sorted by residual: dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CG ARG I 279 " pdb=" CD ARG I 279 " pdb=" NE ARG I 279 " pdb=" CZ ARG I 279 " ideal model delta sinusoidal sigma weight residual 90.00 39.27 50.73 2 1.50e+01 4.44e-03 1.28e+01 dihedral pdb=" CB GLU I 141 " pdb=" CG GLU I 141 " pdb=" CD GLU I 141 " pdb=" OE1 GLU I 141 " ideal model delta sinusoidal sigma weight residual 0.00 -88.57 88.57 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 612 0.045 - 0.090: 129 0.090 - 0.136: 33 0.136 - 0.181: 1 0.181 - 0.226: 2 Chirality restraints: 777 Sorted by residual: chirality pdb=" C20 X1W J 401 " pdb=" C21 X1W J 401 " pdb=" C24 X1W J 401 " pdb=" N19 X1W J 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.68 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C24 X1W J 401 " pdb=" C20 X1W J 401 " pdb=" C23 X1W J 401 " pdb=" O25 X1W J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.90 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA MET I 237 " pdb=" N MET I 237 " pdb=" C MET I 237 " pdb=" CB MET I 237 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 774 not shown) Planarity restraints: 904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP I 116 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" CG ASP I 116 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP I 116 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP I 116 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 165 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO I 166 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 166 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 166 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO J 140 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.019 5.00e-02 4.00e+02 ... (remaining 901 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1258 2.79 - 3.32: 5206 3.32 - 3.84: 9884 3.84 - 4.37: 11771 4.37 - 4.90: 18853 Nonbonded interactions: 46972 Sorted by model distance: nonbonded pdb=" O TRP J 177 " pdb=" O HOH J 501 " model vdw 2.258 2.440 nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.261 2.440 nonbonded pdb=" O ARG I 89 " pdb=" O HOH I 401 " model vdw 2.287 2.440 nonbonded pdb=" O HOH J 504 " pdb=" O HOH J 549 " model vdw 2.304 2.440 nonbonded pdb=" O HOH J 554 " pdb=" O HOH J 557 " model vdw 2.306 2.440 ... (remaining 46967 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.110 Find NCS groups from input model: 0.070 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.005 0.153 5235 Z= 0.287 Angle : 0.615 8.136 7085 Z= 0.298 Chirality : 0.041 0.226 777 Planarity : 0.004 0.036 904 Dihedral : 16.638 88.570 1975 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 16.43 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.97 (0.34), residues: 618 helix: 2.09 (0.29), residues: 335 sheet: 2.90 (1.24), residues: 14 loop : 0.29 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.016 0.001 TYR I 60 ARG 0.009 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.589 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 1.5735 time to fit residues: 167.6401 Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 136 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5235 Z= 0.179 Angle : 0.555 6.892 7085 Z= 0.285 Chirality : 0.040 0.135 777 Planarity : 0.004 0.035 904 Dihedral : 6.466 82.670 720 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.62 % Allowed : 15.16 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.96 (0.35), residues: 618 helix: 2.03 (0.29), residues: 341 sheet: 2.37 (1.36), residues: 15 loop : 0.34 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.015 0.002 TYR I 2 ARG 0.004 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.634 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 104 average time/residue: 1.7288 time to fit residues: 185.5696 Evaluate side-chains 101 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5235 Z= 0.204 Angle : 0.581 6.595 7085 Z= 0.298 Chirality : 0.041 0.137 777 Planarity : 0.004 0.035 904 Dihedral : 5.375 56.341 715 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.44 % Allowed : 15.70 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.78 (0.34), residues: 618 helix: 1.91 (0.28), residues: 343 sheet: 2.35 (1.38), residues: 15 loop : 0.19 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.020 0.002 PHE I 125 TYR 0.018 0.002 TYR I 2 ARG 0.006 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.627 Fit side-chains REVERT: I 239 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5825 (ptpp) outliers start: 8 outliers final: 3 residues processed: 99 average time/residue: 1.5405 time to fit residues: 157.6426 Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 0.2980 chunk 37 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5235 Z= 0.252 Angle : 0.629 7.109 7085 Z= 0.322 Chirality : 0.043 0.143 777 Planarity : 0.005 0.039 904 Dihedral : 5.367 56.194 714 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.44 % Allowed : 15.34 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.46 (0.34), residues: 618 helix: 1.64 (0.28), residues: 349 sheet: 2.37 (1.38), residues: 15 loop : 0.01 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.022 0.002 PHE I 30 TYR 0.021 0.002 TYR I 2 ARG 0.009 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.615 Fit side-chains REVERT: J 227 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6777 (tt0) outliers start: 8 outliers final: 4 residues processed: 96 average time/residue: 1.4855 time to fit residues: 147.6003 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5235 Z= 0.223 Angle : 0.604 7.413 7085 Z= 0.310 Chirality : 0.042 0.139 777 Planarity : 0.005 0.038 904 Dihedral : 5.331 55.806 714 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.53 % Allowed : 14.44 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.42 (0.34), residues: 618 helix: 1.68 (0.28), residues: 347 sheet: 2.47 (1.44), residues: 15 loop : -0.12 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.020 0.002 PHE I 30 TYR 0.018 0.002 TYR I 2 ARG 0.008 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.535 Fit side-chains REVERT: I 63 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7203 (mmm160) REVERT: I 77 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6912 (mmp80) REVERT: I 229 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6492 (pm20) REVERT: I 239 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5860 (ptpp) REVERT: J 227 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6772 (tt0) outliers start: 14 outliers final: 5 residues processed: 103 average time/residue: 1.5463 time to fit residues: 164.5645 Evaluate side-chains 105 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 266 ASP Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 0.4980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5235 Z= 0.229 Angle : 0.617 7.768 7085 Z= 0.315 Chirality : 0.042 0.140 777 Planarity : 0.005 0.038 904 Dihedral : 5.337 55.871 714 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 2.53 % Allowed : 14.62 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.33 (0.34), residues: 618 helix: 1.66 (0.28), residues: 347 sheet: 0.68 (1.09), residues: 25 loop : -0.15 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.020 0.002 PHE I 30 TYR 0.019 0.002 TYR I 2 ARG 0.008 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.608 Fit side-chains REVERT: I 63 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7203 (mmm160) REVERT: I 77 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6894 (mmp80) REVERT: I 229 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6446 (pm20) REVERT: I 239 LYS cc_start: 0.6101 (OUTLIER) cc_final: 0.5862 (ptpp) REVERT: J 227 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6798 (tt0) outliers start: 14 outliers final: 6 residues processed: 104 average time/residue: 1.5761 time to fit residues: 169.6290 Evaluate side-chains 105 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 266 ASP Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 142 GLN I 155 ASN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5235 Z= 0.321 Angle : 0.710 8.263 7085 Z= 0.362 Chirality : 0.045 0.148 777 Planarity : 0.005 0.041 904 Dihedral : 5.503 56.883 714 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 2.71 % Allowed : 14.80 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.10 (0.34), residues: 618 helix: 1.36 (0.28), residues: 347 sheet: 0.58 (1.05), residues: 25 loop : -0.06 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.022 0.003 PHE I 30 TYR 0.025 0.003 TYR I 2 ARG 0.012 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.652 Fit side-chains REVERT: I 63 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7244 (mmm160) REVERT: I 77 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6929 (mmp80) REVERT: I 229 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: J 227 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6768 (tt0) outliers start: 15 outliers final: 7 residues processed: 98 average time/residue: 1.6252 time to fit residues: 164.5321 Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5235 Z= 0.164 Angle : 0.573 7.618 7085 Z= 0.292 Chirality : 0.041 0.141 777 Planarity : 0.004 0.037 904 Dihedral : 5.247 54.513 714 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.08 % Allowed : 16.79 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.68 (0.35), residues: 618 helix: 1.95 (0.28), residues: 343 sheet: 0.44 (1.09), residues: 26 loop : 0.08 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.016 0.002 TYR I 60 ARG 0.007 0.000 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.630 Fit side-chains REVERT: H 268 ARG cc_start: 0.6914 (ptp90) cc_final: 0.6679 (ptp90) REVERT: I 77 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6889 (mmp80) REVERT: J 227 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6811 (tt0) outliers start: 6 outliers final: 2 residues processed: 97 average time/residue: 1.5581 time to fit residues: 156.2638 Evaluate side-chains 94 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5235 Z= 0.159 Angle : 0.576 8.588 7085 Z= 0.292 Chirality : 0.040 0.140 777 Planarity : 0.004 0.036 904 Dihedral : 5.179 54.247 714 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 0.72 % Allowed : 17.87 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.86 (0.35), residues: 618 helix: 2.09 (0.29), residues: 343 sheet: 0.27 (1.05), residues: 26 loop : 0.21 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.020 0.002 PHE I 30 TYR 0.016 0.002 TYR J 169 ARG 0.008 0.000 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.879 Fit side-chains REVERT: H 268 ARG cc_start: 0.6905 (ptp90) cc_final: 0.6672 (ptp90) REVERT: J 227 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6796 (tt0) outliers start: 4 outliers final: 2 residues processed: 95 average time/residue: 1.5831 time to fit residues: 155.8826 Evaluate side-chains 94 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.5980 chunk 56 optimal weight: 0.0030 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5235 Z= 0.168 Angle : 0.599 8.473 7085 Z= 0.303 Chirality : 0.040 0.139 777 Planarity : 0.004 0.036 904 Dihedral : 5.107 54.214 713 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 0.72 % Allowed : 18.41 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.98 (0.35), residues: 618 helix: 2.18 (0.29), residues: 337 sheet: 0.52 (1.06), residues: 25 loop : 0.30 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.028 0.002 PHE I 125 TYR 0.017 0.002 TYR I 60 ARG 0.009 0.000 ARG I 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.678 Fit side-chains REVERT: H 268 ARG cc_start: 0.6949 (ptp90) cc_final: 0.6681 (ptp90) REVERT: J 227 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6781 (tt0) outliers start: 4 outliers final: 2 residues processed: 94 average time/residue: 1.5055 time to fit residues: 146.5225 Evaluate side-chains 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** 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 = 0.4027 r_free = 0.4027 target = 0.168582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150877 restraints weight = 4818.758| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 0.86 r_work: 0.3702 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5235 Z= 0.294 Angle : 0.730 10.973 7085 Z= 0.368 Chirality : 0.045 0.160 777 Planarity : 0.005 0.037 904 Dihedral : 5.345 56.662 713 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.08 % Allowed : 18.41 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.32 (0.34), residues: 618 helix: 1.62 (0.28), residues: 344 sheet: 0.51 (1.05), residues: 25 loop : -0.05 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.029 0.003 PHE I 125 TYR 0.022 0.003 TYR I 2 ARG 0.011 0.001 ARG I 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3116.76 seconds wall clock time: 55 minutes 2.89 seconds (3302.89 seconds total)