Starting phenix.real_space_refine on Thu Jul 2 01:18:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6w_17509/07_2026/8p6w_17509.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6w_17509/07_2026/8p6w_17509.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/8p6w_17509/07_2026/8p6w_17509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6w_17509/07_2026/8p6w_17509.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6w_17509/07_2026/8p6w_17509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6w_17509/07_2026/8p6w_17509.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= 0.001 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 3291 2.51 5 N 870 2.21 5 O 1051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5243 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'X2H': 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "J" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Time building chain proxies: 1.38, per 1000 atoms: 0.26 Number of scatterers: 5243 At special positions: 0 Unit cell: (84.7875, 92.625, 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 1051 8.00 N 870 7.00 C 3291 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: 0.52 Conformation dependent library (CDL) restraints added in 205.3 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: 35 helices and 3 sheets defined 62.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'H' and resid 262 through 264 No H-bonds generated for 'chain 'H' and resid 262 through 264' Processing helix chain 'H' and resid 265 through 270 Processing helix chain 'H' and resid 271 through 275 removed outlier: 3.550A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.857A 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 removed outlier: 3.554A pdb=" N VAL I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.887A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.674A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.713A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.652A 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 200 Processing helix chain 'I' and resid 202 through 207 Processing helix chain 'I' and resid 208 through 225 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.520A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 262 removed outlier: 3.624A pdb=" N LEU I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) 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 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' 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: 3.858A 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: 7.681A pdb=" N LEU J 15 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ARG J 30 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.654A 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 134 275 hydrogen bonds defined for protein. 783 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: 0.82 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1639 1.34 - 1.46: 1098 1.46 - 1.58: 2441 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 5227 Sorted by residual: bond pdb=" C28 X2H J 401 " pdb=" N07 X2H J 401 " ideal model delta sigma weight residual 1.453 1.294 0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C18 X2H J 401 " pdb=" N19 X2H J 401 " ideal model delta sigma weight residual 1.388 1.455 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C08 X2H J 401 " pdb=" N07 X2H J 401 " ideal model delta sigma weight residual 1.417 1.351 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C08 X2H J 401 " pdb=" N09 X2H J 401 " ideal model delta sigma weight residual 1.389 1.449 -0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" C18 X2H J 401 " pdb=" N27 X2H J 401 " ideal model delta sigma weight residual 1.378 1.325 0.053 2.00e-02 2.50e+03 7.14e+00 ... (remaining 5222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 6952 2.24 - 4.47: 110 4.47 - 6.71: 8 6.71 - 8.94: 1 8.94 - 11.18: 1 Bond angle restraints: 7072 Sorted by residual: angle pdb=" CB MET H 265 " pdb=" CG MET H 265 " pdb=" SD MET H 265 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 108.63 5.27 1.80e+00 3.09e-01 8.57e+00 angle pdb=" CB MET I 54 " pdb=" CG MET I 54 " pdb=" SD MET I 54 " ideal model delta sigma weight residual 112.70 119.68 -6.98 3.00e+00 1.11e-01 5.41e+00 angle pdb=" CB GLU J 95 " pdb=" CG GLU J 95 " pdb=" CD GLU J 95 " ideal model delta sigma weight residual 112.60 116.32 -3.72 1.70e+00 3.46e-01 4.80e+00 angle pdb=" C VAL J 173 " pdb=" N VAL J 174 " pdb=" CA VAL J 174 " ideal model delta sigma weight residual 121.97 125.63 -3.66 1.80e+00 3.09e-01 4.15e+00 ... (remaining 7067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 2792 17.81 - 35.62: 266 35.62 - 53.43: 77 53.43 - 71.24: 16 71.24 - 89.05: 9 Dihedral angle restraints: 3160 sinusoidal: 1313 harmonic: 1847 Sorted by residual: 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 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 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 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ILE I 180 " pdb=" C ILE I 180 " pdb=" N LEU I 181 " pdb=" CA LEU I 181 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 436 0.029 - 0.057: 217 0.057 - 0.086: 74 0.086 - 0.115: 37 0.115 - 0.144: 11 Chirality restraints: 775 Sorted by residual: 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 5.16e-01 chirality pdb=" CA PRO J 238 " pdb=" N PRO J 238 " pdb=" C PRO J 238 " pdb=" CB PRO J 238 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CG LEU I 65 " pdb=" CB LEU I 65 " pdb=" CD1 LEU I 65 " pdb=" CD2 LEU I 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 772 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 71 " -0.015 2.00e-02 2.50e+03 1.08e-02 2.03e+00 pdb=" CG PHE I 71 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE I 71 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE I 71 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE I 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 71 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE I 71 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+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 delta sigma weight rms_deltas residual plane pdb=" C THR J 231 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO J 232 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO J 232 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 232 " 0.019 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1123 2.77 - 3.30: 5324 3.30 - 3.84: 9941 3.84 - 4.37: 11799 4.37 - 4.90: 19099 Nonbonded interactions: 47286 Sorted by model distance: nonbonded pdb=" OE2 GLU J 62 " pdb=" O HOH J 501 " model vdw 2.239 3.040 nonbonded pdb=" O LEU J 290 " pdb=" O HOH J 502 " model vdw 2.248 3.040 nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 401 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR J 233 " pdb=" OE1 GLU J 235 " model vdw 2.261 3.040 nonbonded pdb=" O HOH H 405 " pdb=" O HOH J 555 " model vdw 2.263 3.040 ... (remaining 47281 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: 4.690 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.010 Find NCS groups from input model: 0.030 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:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 0.159 5227 Z= 0.247 Angle : 0.656 11.179 7072 Z= 0.331 Chirality : 0.042 0.144 775 Planarity : 0.005 0.035 903 Dihedral : 16.088 89.046 1964 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 0.90 % Allowed : 14.98 % Favored : 84.12 % 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 are not related in a simple way. whole: 1.39 (0.33), residues: 618 helix: 1.60 (0.27), residues: 344 sheet: 1.06 (2.27), residues: 5 loop : 0.12 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 77 TYR 0.021 0.002 TYR I 91 PHE 0.023 0.003 PHE I 71 TRP 0.014 0.003 TRP J 132 HIS 0.006 0.002 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.25 ( 5227) covalent geometry : angle 0.65617 / 0.33 ( 7072) hydrogen bonds : bond 0.11408 / 7.27 ( 275) hydrogen bonds : angle 5.97850 / 4.24 ( 783) *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.199 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 104 average time/residue: 0.6909 time to fit residues: 74.3467 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 : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 244 CYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN J 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.192047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173964 restraints weight = 3679.819| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 0.55 r_work: 0.3812 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work: 0.3638 rms_B_bonded: 4.25 restraints_weight: 0.1250 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.0660 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= 0.138 Angle : 0.549 6.227 7072 Z= 0.286 Chirality : 0.040 0.140 775 Planarity : 0.004 0.033 903 Dihedral : 5.222 53.361 708 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.44 % Allowed : 13.90 % Favored : 84.66 % 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 are not related in a simple way. whole: 1.83 (0.34), residues: 618 helix: 2.01 (0.28), residues: 343 sheet: -0.07 (1.26), residues: 15 loop : 0.31 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 77 TYR 0.020 0.002 TYR I 91 PHE 0.015 0.002 PHE I 71 TRP 0.010 0.001 TRP I 11 HIS 0.006 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 5227) covalent geometry : angle 0.54887 / 0.29 ( 7072) hydrogen bonds : bond 0.05092 / 3.23 ( 275) hydrogen bonds : angle 4.94265 / 3.48 ( 783) *********************** 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 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: H 262 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6951 (mm-30) outliers start: 8 outliers final: 2 residues processed: 105 average time/residue: 0.6345 time to fit residues: 69.0418 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 244 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.191364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173930 restraints weight = 3662.881| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 0.53 r_work: 0.3817 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work: 0.3644 rms_B_bonded: 4.00 restraints_weight: 0.1250 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5227 Z= 0.157 Angle : 0.567 6.167 7072 Z= 0.297 Chirality : 0.041 0.140 775 Planarity : 0.005 0.033 903 Dihedral : 5.125 54.804 703 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.62 % Allowed : 13.90 % Favored : 84.48 % 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 are not related in a simple way. whole: 1.78 (0.33), residues: 618 helix: 1.95 (0.27), residues: 343 sheet: 1.53 (2.64), residues: 5 loop : 0.25 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 9 TYR 0.020 0.002 TYR I 91 PHE 0.017 0.002 PHE I 71 TRP 0.013 0.002 TRP I 11 HIS 0.007 0.001 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 5227) covalent geometry : angle 0.56737 / 0.30 ( 7072) hydrogen bonds : bond 0.05219 / 3.33 ( 275) hydrogen bonds : angle 4.95132 / 3.48 ( 783) *********************** 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 112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.212 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 107 average time/residue: 0.6416 time to fit residues: 71.1733 Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 189 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN 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 = 0.191657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.173442 restraints weight = 3653.480| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 0.55 r_work: 0.3803 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work: 0.3625 rms_B_bonded: 4.32 restraints_weight: 0.1250 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5227 Z= 0.144 Angle : 0.555 6.770 7072 Z= 0.288 Chirality : 0.040 0.140 775 Planarity : 0.004 0.033 903 Dihedral : 4.846 54.449 702 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 14.62 % Favored : 84.30 % 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 are not related in a simple way. whole: 1.86 (0.33), residues: 618 helix: 2.05 (0.27), residues: 342 sheet: 1.62 (2.68), residues: 5 loop : 0.24 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 77 TYR 0.020 0.002 TYR I 91 PHE 0.015 0.002 PHE I 71 TRP 0.012 0.002 TRP I 11 HIS 0.006 0.001 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 5227) covalent geometry : angle 0.55473 / 0.29 ( 7072) hydrogen bonds : bond 0.04965 / 3.16 ( 275) hydrogen bonds : angle 4.84849 / 3.42 ( 783) *********************** 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: 6 poor density : 100 time to evaluate : 0.201 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 102 average time/residue: 0.6374 time to fit residues: 67.3984 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 189 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.190761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172226 restraints weight = 3703.417| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 0.55 r_work: 0.3793 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work: 0.3611 rms_B_bonded: 4.25 restraints_weight: 0.1250 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5227 Z= 0.171 Angle : 0.596 9.453 7072 Z= 0.309 Chirality : 0.042 0.140 775 Planarity : 0.005 0.034 903 Dihedral : 4.970 54.913 702 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 0.90 % Allowed : 14.80 % Favored : 84.30 % 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 are not related in a simple way. whole: 1.68 (0.33), residues: 618 helix: 1.88 (0.27), residues: 343 sheet: 1.54 (2.60), residues: 5 loop : 0.19 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 77 TYR 0.021 0.002 TYR I 91 PHE 0.019 0.003 PHE I 71 TRP 0.014 0.002 TRP I 11 HIS 0.007 0.001 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 5227) covalent geometry : angle 0.59636 / 0.31 ( 7072) hydrogen bonds : bond 0.05320 / 3.40 ( 275) hydrogen bonds : angle 4.97374 / 3.49 ( 783) *********************** 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: 5 poor density : 97 time to evaluate : 0.125 Fit side-chains REVERT: J 13 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6130 (pt0) outliers start: 5 outliers final: 3 residues processed: 99 average time/residue: 0.6823 time to fit residues: 69.8825 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 13 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 4 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.191400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.173147 restraints weight = 3713.848| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 0.55 r_work: 0.3794 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work: 0.3616 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0784 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= 0.152 Angle : 0.577 10.429 7072 Z= 0.297 Chirality : 0.041 0.140 775 Planarity : 0.005 0.033 903 Dihedral : 4.896 54.878 702 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 0.90 % Allowed : 15.16 % 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 are not related in a simple way. whole: 1.76 (0.33), residues: 618 helix: 1.96 (0.27), residues: 343 sheet: 1.59 (2.68), residues: 5 loop : 0.19 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 77 TYR 0.020 0.002 TYR I 91 PHE 0.017 0.002 PHE I 71 TRP 0.012 0.002 TRP I 11 HIS 0.006 0.001 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 5227) covalent geometry : angle 0.57681 / 0.30 ( 7072) hydrogen bonds : bond 0.05063 / 3.23 ( 275) hydrogen bonds : angle 4.87212 / 3.43 ( 783) *********************** 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: J 13 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6081 (pt0) outliers start: 5 outliers final: 3 residues processed: 97 average time/residue: 0.6463 time to fit residues: 64.8552 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 13 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN J 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.193303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.175231 restraints weight = 3724.079| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 0.55 r_work: 0.3822 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work: 0.3645 rms_B_bonded: 4.43 restraints_weight: 0.1250 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1018 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= 0.120 Angle : 0.523 6.509 7072 Z= 0.273 Chirality : 0.040 0.141 775 Planarity : 0.004 0.034 903 Dihedral : 4.713 53.654 702 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 0.90 % Allowed : 15.16 % 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 are not related in a simple way. whole: 2.02 (0.34), residues: 618 helix: 2.30 (0.28), residues: 337 sheet: -0.10 (1.38), residues: 15 loop : 0.23 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 77 TYR 0.018 0.002 TYR I 91 PHE 0.014 0.002 PHE J 185 TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 5227) covalent geometry : angle 0.52303 / 0.27 ( 7072) hydrogen bonds : bond 0.04528 / 2.89 ( 275) hydrogen bonds : angle 4.66491 / 3.30 ( 783) *********************** 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: J 13 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.6044 (pt0) outliers start: 5 outliers final: 0 residues processed: 99 average time/residue: 0.5529 time to fit residues: 56.7168 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 13 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.0570 chunk 33 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 0.0010 chunk 13 optimal weight: 0.0470 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.196358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.178557 restraints weight = 3744.244| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 0.55 r_work: 0.3862 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work: 0.3681 rms_B_bonded: 4.62 restraints_weight: 0.1250 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5227 Z= 0.103 Angle : 0.505 9.532 7072 Z= 0.258 Chirality : 0.039 0.138 775 Planarity : 0.004 0.038 903 Dihedral : 4.543 53.505 702 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 0.72 % Allowed : 16.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.34), residues: 618 helix: 2.44 (0.28), residues: 337 sheet: 0.11 (1.37), residues: 15 loop : 0.26 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 77 TYR 0.016 0.001 TYR I 91 PHE 0.013 0.001 PHE I 110 TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 5227) covalent geometry : angle 0.50527 / 0.26 ( 7072) hydrogen bonds : bond 0.04003 / 2.55 ( 275) hydrogen bonds : angle 4.43059 / 3.14 ( 783) *********************** 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 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: J 13 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.6034 (pt0) outliers start: 4 outliers final: 1 residues processed: 94 average time/residue: 0.5159 time to fit residues: 50.2255 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 13 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN H 281 GLN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.191758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.173440 restraints weight = 3659.721| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 0.55 r_work: 0.3804 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work: 0.3627 rms_B_bonded: 4.27 restraints_weight: 0.1250 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5227 Z= 0.160 Angle : 0.585 5.791 7072 Z= 0.304 Chirality : 0.041 0.137 775 Planarity : 0.005 0.034 903 Dihedral : 4.888 54.736 702 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 0.54 % Allowed : 16.43 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.33), residues: 618 helix: 2.02 (0.28), residues: 343 sheet: 1.14 (2.36), residues: 5 loop : 0.25 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 77 TYR 0.021 0.002 TYR I 91 PHE 0.024 0.003 PHE J 185 TRP 0.014 0.002 TRP I 11 HIS 0.007 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 5227) covalent geometry : angle 0.58521 / 0.30 ( 7072) hydrogen bonds : bond 0.05095 / 3.25 ( 275) hydrogen bonds : angle 4.83067 / 3.41 ( 783) *********************** 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.202 Fit side-chains REVERT: J 13 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.6083 (pt0) outliers start: 3 outliers final: 1 residues processed: 100 average time/residue: 0.6502 time to fit residues: 67.3291 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.193427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.175314 restraints weight = 3732.445| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 0.55 r_work: 0.3828 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work: 0.3652 rms_B_bonded: 4.32 restraints_weight: 0.1250 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1106 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= 0.124 Angle : 0.537 6.690 7072 Z= 0.279 Chirality : 0.040 0.139 775 Planarity : 0.004 0.036 903 Dihedral : 4.748 53.946 702 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 0.36 % Allowed : 16.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.33), residues: 618 helix: 2.29 (0.28), residues: 337 sheet: -0.13 (1.28), residues: 15 loop : 0.28 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 77 TYR 0.019 0.002 TYR I 91 PHE 0.019 0.002 PHE J 185 TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 5227) covalent geometry : angle 0.53716 / 0.28 ( 7072) hydrogen bonds : bond 0.04567 / 2.92 ( 275) hydrogen bonds : angle 4.62589 / 3.27 ( 783) ********************** 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.164 Fit side-chains REVERT: J 13 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.6054 (pt0) outliers start: 2 outliers final: 1 residues processed: 98 average time/residue: 0.6131 time to fit residues: 62.1429 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 chunk 59 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 10 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.9818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 281 GLN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.192413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.174042 restraints weight = 3736.574| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 0.55 r_work: 0.3817 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work: 0.3635 rms_B_bonded: 4.30 restraints_weight: 0.1250 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5227 Z= 0.142 Angle : 0.565 6.647 7072 Z= 0.294 Chirality : 0.041 0.137 775 Planarity : 0.005 0.034 903 Dihedral : 4.847 54.552 702 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 0.36 % Allowed : 16.61 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.33), residues: 618 helix: 2.05 (0.28), residues: 343 sheet: 1.35 (2.09), residues: 5 loop : 0.27 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 77 TYR 0.020 0.002 TYR I 91 PHE 0.023 0.002 PHE J 185 TRP 0.012 0.002 TRP I 11 HIS 0.006 0.001 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 5227) covalent geometry : angle 0.56490 / 0.29 ( 7072) hydrogen bonds : bond 0.04858 / 3.10 ( 275) hydrogen bonds : angle 4.74515 / 3.36 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.03 seconds wall clock time: 53 minutes 43.47 seconds (3223.47 seconds total)