Starting phenix.real_space_refine on Thu Nov 14 08:49:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/11_2024/8p76_17519.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/11_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_17519/11_2024/8p76_17519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/11_2024/8p76_17519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/11_2024/8p76_17519.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/11_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. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.51, per 1000 atoms: 0.86 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 - 3.00 Amino acid : True - 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: 1.57 Conformation dependent library (CDL) restraints added in 676.7 milliseconds 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: 0.52 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: 1.41 Time building geometry restraints manager: 1.65 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: 0.00 - 1.63: 6917 1.63 - 3.25: 128 3.25 - 4.88: 27 4.88 - 6.51: 8 6.51 - 8.14: 5 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 3.040 nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.261 3.040 nonbonded pdb=" O ARG I 89 " pdb=" O HOH I 401 " model vdw 2.287 3.040 nonbonded pdb=" O HOH J 504 " pdb=" O HOH J 549 " model vdw 2.304 3.040 nonbonded pdb=" O HOH J 554 " pdb=" O HOH J 557 " model vdw 2.306 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 3.900 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.190 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:14.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.220 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.607 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 1.6924 time to fit residues: 180.0763 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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: 3.9990 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 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: 0.7819 moved from start: 0.0627 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= 0.210 Angle : 0.590 6.964 7085 Z= 0.302 Chirality : 0.042 0.139 777 Planarity : 0.005 0.034 904 Dihedral : 6.449 82.183 720 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 14.44 % Favored : 83.94 % 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: 1.85 (0.35), residues: 618 helix: 1.93 (0.29), residues: 341 sheet: 2.29 (1.35), residues: 15 loop : 0.31 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.020 0.002 PHE I 30 TYR 0.017 0.002 TYR I 2 ARG 0.006 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 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.727 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 104 average time/residue: 1.6836 time to fit residues: 181.1089 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL 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: 1.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7819 moved from start: 0.0714 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= 0.206 Angle : 0.580 6.707 7085 Z= 0.297 Chirality : 0.041 0.138 777 Planarity : 0.004 0.035 904 Dihedral : 5.320 56.202 714 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.44 % Allowed : 14.98 % Favored : 83.57 % 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: 1.74 (0.34), residues: 618 helix: 1.88 (0.28), residues: 343 sheet: 2.27 (1.40), residues: 15 loop : 0.18 (0.40), residues: 260 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 0.019 0.002 PHE I 30 TYR 0.017 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 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.576 Fit side-chains REVERT: I 239 LYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5775 (ptpp) outliers start: 8 outliers final: 5 residues processed: 101 average time/residue: 1.7094 time to fit residues: 178.4767 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 239 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.0745 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= 0.179 Angle : 0.556 6.956 7085 Z= 0.284 Chirality : 0.040 0.138 777 Planarity : 0.004 0.036 904 Dihedral : 5.245 55.735 714 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % 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: 1.86 (0.35), residues: 618 helix: 1.98 (0.28), residues: 343 sheet: 2.33 (1.42), residues: 15 loop : 0.22 (0.40), residues: 260 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 0.018 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.005 0.001 ARG I 279 *********************** 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 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.628 Fit side-chains REVERT: J 227 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6740 (tt0) outliers start: 8 outliers final: 5 residues processed: 101 average time/residue: 1.6766 time to fit residues: 175.4924 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0270 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- 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** J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0798 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= 0.232 Angle : 0.610 7.420 7085 Z= 0.312 Chirality : 0.042 0.139 777 Planarity : 0.005 0.036 904 Dihedral : 5.331 56.432 714 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.62 % Allowed : 15.70 % 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: 1.66 (0.34), residues: 618 helix: 1.82 (0.28), residues: 343 sheet: 2.37 (1.41), residues: 15 loop : 0.12 (0.40), residues: 260 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 0.019 0.002 PHE I 30 TYR 0.019 0.002 TYR I 2 ARG 0.007 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.667 Fit side-chains REVERT: I 239 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.5785 (ptpp) REVERT: J 227 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6793 (tt0) outliers start: 9 outliers final: 5 residues processed: 97 average time/residue: 1.6685 time to fit residues: 167.1175 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 239 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.0773 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= 0.176 Angle : 0.562 7.718 7085 Z= 0.287 Chirality : 0.040 0.140 777 Planarity : 0.004 0.036 904 Dihedral : 5.226 55.611 714 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.44 % Allowed : 16.06 % 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: 1.85 (0.35), residues: 618 helix: 2.00 (0.28), residues: 343 sheet: 2.36 (1.43), residues: 15 loop : 0.18 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.016 0.002 TYR I 60 ARG 0.006 0.001 ARG I 279 *********************** 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 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.621 Fit side-chains REVERT: J 227 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6769 (tt0) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 1.5898 time to fit residues: 167.8681 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5235 Z= 0.285 Angle : 0.662 8.195 7085 Z= 0.337 Chirality : 0.044 0.144 777 Planarity : 0.005 0.038 904 Dihedral : 5.421 57.004 714 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 15.34 % 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: 1.43 (0.34), residues: 618 helix: 1.70 (0.28), residues: 342 sheet: 0.75 (1.07), residues: 25 loop : -0.00 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.025 0.003 PHE I 125 TYR 0.022 0.002 TYR I 2 ARG 0.009 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.636 Fit side-chains REVERT: I 33 LYS cc_start: 0.7221 (ttpp) cc_final: 0.6886 (mptt) REVERT: I 63 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7243 (mmm160) REVERT: I 239 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5812 (ptpp) REVERT: J 227 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6811 (tt0) outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 1.5915 time to fit residues: 161.4347 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 227 GLU 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: 5.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5235 Z= 0.280 Angle : 0.674 8.936 7085 Z= 0.342 Chirality : 0.044 0.144 777 Planarity : 0.005 0.045 904 Dihedral : 5.455 56.633 714 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.99 % Allowed : 15.52 % 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: 1.20 (0.34), residues: 618 helix: 1.51 (0.28), residues: 347 sheet: 2.11 (1.34), residues: 15 loop : -0.21 (0.38), residues: 256 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 0.003 PHE I 125 TYR 0.021 0.002 TYR I 2 ARG 0.010 0.001 ARG I 23 *********************** 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.620 Fit side-chains REVERT: I 33 LYS cc_start: 0.7195 (ttpp) cc_final: 0.6902 (mptt) REVERT: I 63 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7239 (mmm160) REVERT: I 239 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5839 (ptpp) REVERT: J 227 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6814 (tt0) outliers start: 11 outliers final: 5 residues processed: 97 average time/residue: 1.6868 time to fit residues: 169.1889 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 120 VAL 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 251 SER 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: 0.7980 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5235 Z= 0.274 Angle : 0.684 9.974 7085 Z= 0.348 Chirality : 0.044 0.144 777 Planarity : 0.005 0.051 904 Dihedral : 5.470 56.522 714 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.81 % Allowed : 15.70 % 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: 1.30 (0.34), residues: 618 helix: 1.63 (0.28), residues: 341 sheet: 0.28 (1.02), residues: 26 loop : -0.07 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.021 0.002 PHE I 125 TYR 0.021 0.002 TYR I 2 ARG 0.010 0.001 ARG I 23 *********************** 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.633 Fit side-chains REVERT: I 33 LYS cc_start: 0.7195 (ttpp) cc_final: 0.6905 (mptt) REVERT: I 63 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7239 (mmm160) REVERT: I 239 LYS cc_start: 0.6113 (OUTLIER) cc_final: 0.5856 (ptpp) REVERT: J 227 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6803 (tt0) outliers start: 10 outliers final: 4 residues processed: 97 average time/residue: 1.6980 time to fit residues: 169.9522 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 227 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 0.0070 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5235 Z= 0.172 Angle : 0.598 8.743 7085 Z= 0.304 Chirality : 0.041 0.142 777 Planarity : 0.004 0.036 904 Dihedral : 5.280 54.738 714 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 16.25 % Favored : 82.31 % 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 (0.35), residues: 618 helix: 2.11 (0.29), residues: 337 sheet: 0.37 (1.04), residues: 26 loop : 0.06 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.021 0.002 PHE I 125 TYR 0.020 0.002 TYR H 287 ARG 0.008 0.001 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.612 Fit side-chains REVERT: I 33 LYS cc_start: 0.7180 (ttpp) cc_final: 0.6880 (mptt) REVERT: J 227 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6818 (tt0) outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 1.5497 time to fit residues: 162.0350 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.170405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.152633 restraints weight = 4832.923| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 0.87 r_work: 0.3736 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5235 Z= 0.190 Angle : 0.627 8.898 7085 Z= 0.317 Chirality : 0.041 0.146 777 Planarity : 0.005 0.037 904 Dihedral : 5.279 55.142 714 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 16.97 % Favored : 81.95 % 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: 1.80 (0.35), residues: 618 helix: 2.09 (0.28), residues: 337 sheet: 0.65 (1.06), residues: 25 loop : 0.10 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.021 0.002 PHE I 125 TYR 0.019 0.002 TYR H 287 ARG 0.008 0.001 ARG I 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3137.04 seconds wall clock time: 57 minutes 26.53 seconds (3446.53 seconds total)