Starting phenix.real_space_refine on Fri Oct 10 12:39:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p72_17515/10_2025/8p72_17515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p72_17515/10_2025/8p72_17515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p72_17515/10_2025/8p72_17515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p72_17515/10_2025/8p72_17515.map" model { file = "/net/cci-nas-00/data/ceres_data/8p72_17515/10_2025/8p72_17515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p72_17515/10_2025/8p72_17515.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 3290 2.51 5 N 870 2.21 5 O 1036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5227 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'X2Z': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "I" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Time building chain proxies: 1.57, per 1000 atoms: 0.30 Number of scatterers: 5227 At special positions: 0 Unit cell: (82.65, 94.05, 67.6875, 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 1036 8.00 N 870 7.00 C 3290 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: 0.41 Conformation dependent library (CDL) restraints added in 193.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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 4 sheets defined 61.7% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'H' and resid 263 through 267 removed outlier: 4.042A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 275 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 38 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.914A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.931A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 129 removed outlier: 3.862A pdb=" N LEU I 129 " --> pdb=" O PHE I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.707A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.555A 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 186 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.682A 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: 3.795A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 262 Processing helix chain 'I' and resid 266 through 283 removed outlier: 3.862A pdb=" N ALA I 283 " --> pdb=" O ARG I 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 68 removed outlier: 3.899A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) 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: 3.959A 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 14 removed outlier: 3.562A pdb=" N GLU J 13 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 13 through 14 removed outlier: 3.562A pdb=" N GLU J 13 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'J' and resid 133 through 134 277 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.55 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: 1641 1.34 - 1.46: 1038 1.46 - 1.58: 2499 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 5227 Sorted by residual: bond pdb=" C08 X2Z J 401 " pdb=" N09 X2Z J 401 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C18 X2Z J 401 " pdb=" N19 X2Z J 401 " ideal model delta sigma weight residual 1.363 1.449 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C27 X2Z J 401 " pdb=" N07 X2Z J 401 " ideal model delta sigma weight residual 1.386 1.302 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C20 X2Z J 401 " pdb=" C21 X2Z J 401 " ideal model delta sigma weight residual 1.528 1.479 0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C21 X2Z J 401 " pdb=" C22 X2Z J 401 " ideal model delta sigma weight residual 1.530 1.482 0.048 2.00e-02 2.50e+03 5.68e+00 ... (remaining 5222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 6816 1.40 - 2.79: 193 2.79 - 4.19: 47 4.19 - 5.58: 11 5.58 - 6.98: 7 Bond angle restraints: 7074 Sorted by residual: angle pdb=" CA LYS J 293 " pdb=" CB LYS J 293 " pdb=" CG LYS J 293 " ideal model delta sigma weight residual 114.10 119.95 -5.85 2.00e+00 2.50e-01 8.56e+00 angle pdb=" CA LYS I 189 " pdb=" CB LYS I 189 " pdb=" CG LYS I 189 " ideal model delta sigma weight residual 114.10 119.10 -5.00 2.00e+00 2.50e-01 6.26e+00 angle pdb=" CB LYS I 253 " pdb=" CG LYS I 253 " pdb=" CD LYS I 253 " ideal model delta sigma weight residual 111.30 117.01 -5.71 2.30e+00 1.89e-01 6.16e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.61 4.29 1.80e+00 3.09e-01 5.67e+00 angle pdb=" CB MET J 94 " pdb=" CG MET J 94 " pdb=" SD MET J 94 " ideal model delta sigma weight residual 112.70 119.68 -6.98 3.00e+00 1.11e-01 5.41e+00 ... (remaining 7069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2748 17.44 - 34.88: 301 34.88 - 52.32: 86 52.32 - 69.76: 18 69.76 - 87.21: 11 Dihedral angle restraints: 3164 sinusoidal: 1317 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 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG I 197 " pdb=" CD ARG I 197 " pdb=" NE ARG I 197 " pdb=" CZ ARG I 197 " ideal model delta sinusoidal sigma weight residual 180.00 -136.20 -43.80 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA THR I 176 " pdb=" C THR I 176 " pdb=" N ARG I 177 " pdb=" CA ARG I 177 " ideal model delta harmonic sigma weight residual -180.00 -164.26 -15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 3161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 459 0.028 - 0.055: 191 0.055 - 0.083: 76 0.083 - 0.110: 36 0.110 - 0.138: 14 Chirality restraints: 776 Sorted by residual: chirality pdb=" CG LEU I 236 " pdb=" CB LEU I 236 " pdb=" CD1 LEU I 236 " pdb=" CD2 LEU I 236 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 773 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU I 49 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO I 50 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU I 141 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" CD GLU I 141 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU I 141 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU I 141 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO I 163 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.021 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 732 2.75 - 3.29: 5361 3.29 - 3.83: 9925 3.83 - 4.36: 11676 4.36 - 4.90: 19254 Nonbonded interactions: 46948 Sorted by model distance: nonbonded pdb=" O HOH J 501 " pdb=" O HOH J 537 " model vdw 2.215 3.040 nonbonded pdb=" OG SER I 78 " pdb=" OD2 ASP I 116 " model vdw 2.220 3.040 nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.225 3.040 nonbonded pdb=" O PRO J 280 " pdb=" O HOH J 501 " model vdw 2.256 3.040 nonbonded pdb=" O HOH J 544 " pdb=" O HOH J 550 " model vdw 2.273 3.040 ... (remaining 46943 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: 3.950 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.050 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.004 0.110 5227 Z= 0.191 Angle : 0.615 6.981 7074 Z= 0.308 Chirality : 0.041 0.138 776 Planarity : 0.005 0.038 903 Dihedral : 16.505 87.206 1968 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 0.54 % Allowed : 18.23 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.33), residues: 618 helix: 1.91 (0.28), residues: 339 sheet: -0.00 (1.28), residues: 16 loop : -0.09 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 256 TYR 0.016 0.002 TYR I 91 PHE 0.019 0.002 PHE I 30 TRP 0.012 0.001 TRP I 11 HIS 0.004 0.001 HIS I 161 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5227) covalent geometry : angle 0.61502 ( 7074) hydrogen bonds : bond 0.14784 ( 276) hydrogen bonds : angle 5.83157 ( 774) *********************** 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 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.221 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 92 average time/residue: 0.8410 time to fit residues: 79.6470 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 142 GLN ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS ** J 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.187363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166097 restraints weight = 4590.524| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 0.88 r_work: 0.3863 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5227 Z= 0.157 Angle : 0.596 5.717 7074 Z= 0.311 Chirality : 0.042 0.134 776 Planarity : 0.005 0.037 903 Dihedral : 4.995 56.009 709 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.53 % Allowed : 15.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.33), residues: 618 helix: 1.97 (0.27), residues: 337 sheet: 0.64 (1.41), residues: 15 loop : -0.04 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 188 TYR 0.019 0.002 TYR I 91 PHE 0.017 0.002 PHE I 30 TRP 0.011 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5227) covalent geometry : angle 0.59641 ( 7074) hydrogen bonds : bond 0.05479 ( 276) hydrogen bonds : angle 4.97309 ( 774) *********************** 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: I 49 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5471 (mp0) REVERT: I 119 ASN cc_start: 0.6947 (m-40) cc_final: 0.6743 (m110) REVERT: I 234 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5539 (mm-30) REVERT: J 10 LYS cc_start: 0.4754 (OUTLIER) cc_final: 0.4478 (tptp) outliers start: 14 outliers final: 4 residues processed: 95 average time/residue: 0.7548 time to fit residues: 74.0492 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 247 GLN Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 158 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 183 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.183580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162154 restraints weight = 4553.603| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 0.88 r_work: 0.3819 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 5227 Z= 0.308 Angle : 0.781 6.559 7074 Z= 0.410 Chirality : 0.049 0.157 776 Planarity : 0.007 0.045 903 Dihedral : 5.555 56.824 708 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.89 % Allowed : 13.72 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.32), residues: 618 helix: 1.15 (0.26), residues: 337 sheet: 1.02 (1.43), residues: 15 loop : -0.37 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 188 TYR 0.020 0.003 TYR I 91 PHE 0.027 0.003 PHE I 71 TRP 0.017 0.004 TRP I 11 HIS 0.009 0.002 HIS I 281 Details of bonding type rmsd covalent geometry : bond 0.00682 ( 5227) covalent geometry : angle 0.78057 ( 7074) hydrogen bonds : bond 0.06932 ( 276) hydrogen bonds : angle 5.27755 ( 774) *********************** 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.218 Fit side-chains REVERT: I 234 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5465 (mm-30) outliers start: 16 outliers final: 3 residues processed: 93 average time/residue: 0.6762 time to fit residues: 65.1554 Evaluate side-chains 82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 56 optimal weight: 0.0060 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 183 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.188755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.167793 restraints weight = 4611.871| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 0.88 r_work: 0.3882 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5227 Z= 0.122 Angle : 0.553 5.748 7074 Z= 0.290 Chirality : 0.041 0.135 776 Planarity : 0.005 0.039 903 Dihedral : 5.011 57.695 708 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.26 % Allowed : 14.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.33), residues: 618 helix: 1.92 (0.27), residues: 339 sheet: 0.83 (1.45), residues: 15 loop : -0.08 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 223 TYR 0.017 0.002 TYR I 91 PHE 0.017 0.002 PHE I 30 TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS I 161 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5227) covalent geometry : angle 0.55305 ( 7074) hydrogen bonds : bond 0.04706 ( 276) hydrogen bonds : angle 4.70692 ( 774) *********************** 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.226 Fit side-chains REVERT: I 234 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5367 (mm-30) REVERT: I 279 ARG cc_start: 0.6440 (mtm-85) cc_final: 0.6212 (mtm-85) REVERT: J 292 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7049 (mtp) outliers start: 7 outliers final: 2 residues processed: 94 average time/residue: 0.6667 time to fit residues: 64.8840 Evaluate side-chains 85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 0.0870 chunk 35 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN H 294 HIS I 18 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.186275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.164631 restraints weight = 4700.231| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 0.89 r_work: 0.3847 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5227 Z= 0.176 Angle : 0.620 5.618 7074 Z= 0.325 Chirality : 0.043 0.150 776 Planarity : 0.005 0.041 903 Dihedral : 5.101 58.670 708 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 14.98 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.33), residues: 618 helix: 1.79 (0.27), residues: 337 sheet: 0.91 (1.43), residues: 15 loop : -0.14 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 136 TYR 0.019 0.002 TYR I 91 PHE 0.018 0.002 PHE I 30 TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS I 281 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5227) covalent geometry : angle 0.61996 ( 7074) hydrogen bonds : bond 0.05446 ( 276) hydrogen bonds : angle 4.87911 ( 774) *********************** 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.131 Fit side-chains REVERT: I 49 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5399 (mp0) REVERT: I 234 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5473 (mm-30) outliers start: 9 outliers final: 1 residues processed: 92 average time/residue: 0.7165 time to fit residues: 68.1843 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN I 119 ASN I 183 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN J 258 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.182950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.161365 restraints weight = 4586.972| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 0.88 r_work: 0.3810 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 5227 Z= 0.372 Angle : 0.862 7.151 7074 Z= 0.455 Chirality : 0.053 0.177 776 Planarity : 0.008 0.049 903 Dihedral : 5.460 56.829 706 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.43 % Favored : 97.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.31), residues: 618 helix: 0.69 (0.26), residues: 342 sheet: 1.19 (1.48), residues: 15 loop : -0.52 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG J 136 TYR 0.021 0.004 TYR I 91 PHE 0.029 0.004 PHE I 71 TRP 0.019 0.004 TRP J 237 HIS 0.012 0.003 HIS I 281 Details of bonding type rmsd covalent geometry : bond 0.00824 ( 5227) covalent geometry : angle 0.86247 ( 7074) hydrogen bonds : bond 0.07326 ( 276) hydrogen bonds : angle 5.40305 ( 774) *********************** 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 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.229 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 0.7035 time to fit residues: 62.7226 Evaluate side-chains 85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.188299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.167139 restraints weight = 4623.047| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 0.88 r_work: 0.3875 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5227 Z= 0.129 Angle : 0.576 5.096 7074 Z= 0.304 Chirality : 0.041 0.137 776 Planarity : 0.005 0.042 903 Dihedral : 4.894 59.479 706 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.08 % Allowed : 16.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.33), residues: 618 helix: 1.82 (0.27), residues: 339 sheet: 1.05 (1.48), residues: 15 loop : -0.15 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 223 TYR 0.017 0.002 TYR I 91 PHE 0.021 0.002 PHE I 30 TRP 0.012 0.001 TRP I 11 HIS 0.004 0.001 HIS I 161 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5227) covalent geometry : angle 0.57583 ( 7074) hydrogen bonds : bond 0.04808 ( 276) hydrogen bonds : angle 4.75517 ( 774) *********************** 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 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.244 Fit side-chains REVERT: J 292 MET cc_start: 0.7361 (mtt) cc_final: 0.7065 (mtp) outliers start: 6 outliers final: 1 residues processed: 94 average time/residue: 0.7063 time to fit residues: 68.7946 Evaluate side-chains 82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 186 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.0070 chunk 53 optimal weight: 5.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 183 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.189214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168009 restraints weight = 4637.215| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 0.88 r_work: 0.3883 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5227 Z= 0.125 Angle : 0.573 7.915 7074 Z= 0.300 Chirality : 0.041 0.135 776 Planarity : 0.005 0.042 903 Dihedral : 4.790 59.593 706 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.26 % Allowed : 16.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.34), residues: 618 helix: 2.01 (0.28), residues: 339 sheet: 0.47 (1.38), residues: 16 loop : -0.02 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 256 TYR 0.017 0.002 TYR I 91 PHE 0.019 0.002 PHE I 30 TRP 0.010 0.001 TRP I 11 HIS 0.003 0.001 HIS I 161 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5227) covalent geometry : angle 0.57338 ( 7074) hydrogen bonds : bond 0.04616 ( 276) hydrogen bonds : angle 4.65991 ( 774) *********************** 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.235 Fit side-chains REVERT: I 49 GLU cc_start: 0.5941 (mp0) cc_final: 0.5345 (mp0) REVERT: I 234 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5338 (mm-30) REVERT: J 292 MET cc_start: 0.7356 (mtt) cc_final: 0.7080 (mtp) outliers start: 7 outliers final: 1 residues processed: 94 average time/residue: 0.7152 time to fit residues: 69.4317 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.188050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.166600 restraints weight = 4643.263| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 0.88 r_work: 0.3868 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5227 Z= 0.151 Angle : 0.618 8.094 7074 Z= 0.322 Chirality : 0.042 0.137 776 Planarity : 0.005 0.043 903 Dihedral : 4.851 59.468 706 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 17.87 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.33), residues: 618 helix: 1.90 (0.27), residues: 339 sheet: 0.77 (1.41), residues: 15 loop : -0.05 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 279 TYR 0.018 0.002 TYR I 164 PHE 0.021 0.002 PHE J 252 TRP 0.012 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5227) covalent geometry : angle 0.61828 ( 7074) hydrogen bonds : bond 0.04965 ( 276) hydrogen bonds : angle 4.74089 ( 774) *********************** 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 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.241 Fit side-chains REVERT: I 49 GLU cc_start: 0.5974 (mp0) cc_final: 0.5339 (mp0) REVERT: I 234 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5463 (mm-30) outliers start: 6 outliers final: 2 residues processed: 88 average time/residue: 0.7223 time to fit residues: 65.7060 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.0570 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.191504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.170350 restraints weight = 4666.740| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 0.88 r_work: 0.3914 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5227 Z= 0.116 Angle : 0.573 9.392 7074 Z= 0.297 Chirality : 0.041 0.134 776 Planarity : 0.005 0.042 903 Dihedral : 4.694 59.434 706 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 0.90 % Allowed : 17.51 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.34), residues: 618 helix: 2.12 (0.28), residues: 340 sheet: 0.26 (1.33), residues: 16 loop : 0.06 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 223 TYR 0.016 0.002 TYR I 91 PHE 0.020 0.002 PHE I 30 TRP 0.009 0.001 TRP I 11 HIS 0.003 0.001 HIS J 71 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 5227) covalent geometry : angle 0.57335 ( 7074) hydrogen bonds : bond 0.04264 ( 276) hydrogen bonds : angle 4.54230 ( 774) ********************** 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 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.215 Fit side-chains REVERT: I 234 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5325 (mm-30) REVERT: J 97 ASP cc_start: 0.6904 (p0) cc_final: 0.6693 (p0) REVERT: J 292 MET cc_start: 0.7320 (mtt) cc_final: 0.6962 (mtt) outliers start: 5 outliers final: 1 residues processed: 90 average time/residue: 0.7289 time to fit residues: 67.8414 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.188569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.166915 restraints weight = 4674.723| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 0.89 r_work: 0.3872 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5227 Z= 0.156 Angle : 0.650 9.143 7074 Z= 0.332 Chirality : 0.043 0.134 776 Planarity : 0.005 0.043 903 Dihedral : 4.844 59.512 706 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.44 % Allowed : 16.79 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.34), residues: 618 helix: 1.97 (0.28), residues: 338 sheet: 0.78 (1.39), residues: 15 loop : 0.02 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 223 TYR 0.019 0.002 TYR I 164 PHE 0.019 0.002 PHE I 30 TRP 0.012 0.002 TRP I 11 HIS 0.004 0.001 HIS I 100 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5227) covalent geometry : angle 0.65012 ( 7074) hydrogen bonds : bond 0.05010 ( 276) hydrogen bonds : angle 4.75759 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.91 seconds wall clock time: 51 minutes 10.90 seconds (3070.90 seconds total)