Starting phenix.real_space_refine on Tue Jan 13 10:07:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g4f_29719/01_2026/8g4f_29719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4f_29719/01_2026/8g4f_29719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g4f_29719/01_2026/8g4f_29719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4f_29719/01_2026/8g4f_29719.map" model { file = "/net/cci-nas-00/data/ceres_data/8g4f_29719/01_2026/8g4f_29719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4f_29719/01_2026/8g4f_29719.cif" } resolution = 2.91 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= 0.026 sd= 0.224 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 8 5.16 5 C 1595 2.51 5 N 446 2.21 5 O 509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2561 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1213 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "B" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1316 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Time building chain proxies: 0.80, per 1000 atoms: 0.31 Number of scatterers: 2561 At special positions: 0 Unit cell: (75.328, 53.928, 73.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 8 16.00 P 2 15.00 Mg 1 11.99 O 509 8.00 N 446 7.00 C 1595 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: 0.15 Conformation dependent library (CDL) restraints added in 94.8 milliseconds 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 56.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 202 through 211 Processing helix chain 'A' and resid 212 through 223 removed outlier: 3.736A pdb=" N VAL A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 245 through 255 Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 86 through 105 removed outlier: 3.542A pdb=" N PHE B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 151 through 165 removed outlier: 3.729A pdb=" N PHE B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 46 removed outlier: 3.666A pdb=" N ASP B 38 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR B 4 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU B 56 " --> pdb=" O TYR B 4 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 6 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE B 78 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B 114 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N CYS B 80 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASN B 116 " --> pdb=" O CYS B 80 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE B 82 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ILE B 142 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 113 " --> pdb=" O ILE B 142 " (cutoff:3.500A) 130 hydrogen bonds defined for protein. 384 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: 0.37 Time building geometry restraints manager: 0.21 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: 879 1.34 - 1.46: 401 1.46 - 1.57: 1300 1.57 - 1.69: 3 1.69 - 1.81: 13 Bond restraints: 2596 Sorted by residual: bond pdb=" C5 GDP B 201 " pdb=" C4 GDP B 201 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.36e+00 bond pdb=" CG1 ILE B 24 " pdb=" CD1 ILE B 24 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.73e-01 bond pdb=" CA THR A 268 " pdb=" CB THR A 268 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.73e-02 3.34e+03 3.82e-01 bond pdb=" CB GLU B 49 " pdb=" CG GLU B 49 " ideal model delta sigma weight residual 1.520 1.538 -0.018 3.00e-02 1.11e+03 3.77e-01 bond pdb=" CA VAL A 259 " pdb=" C VAL A 259 " ideal model delta sigma weight residual 1.525 1.518 0.007 1.27e-02 6.20e+03 2.99e-01 ... (remaining 2591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 3431 1.26 - 2.51: 61 2.51 - 3.77: 15 3.77 - 5.03: 3 5.03 - 6.28: 3 Bond angle restraints: 3513 Sorted by residual: angle pdb=" C ILE B 46 " pdb=" N ASP B 47 " pdb=" CA ASP B 47 " ideal model delta sigma weight residual 121.54 125.65 -4.11 1.91e+00 2.74e-01 4.63e+00 angle pdb=" C3' GDP B 201 " pdb=" C2' GDP B 201 " pdb=" C1' GDP B 201 " ideal model delta sigma weight residual 111.00 105.27 5.73 3.00e+00 1.11e-01 3.65e+00 angle pdb=" N ILE B 84 " pdb=" CA ILE B 84 " pdb=" C ILE B 84 " ideal model delta sigma weight residual 113.07 110.55 2.52 1.36e+00 5.41e-01 3.42e+00 angle pdb=" C4' GDP B 201 " pdb=" C3' GDP B 201 " pdb=" C2' GDP B 201 " ideal model delta sigma weight residual 111.00 105.89 5.11 3.00e+00 1.11e-01 2.91e+00 angle pdb=" N GLY B 48 " pdb=" CA GLY B 48 " pdb=" C GLY B 48 " ideal model delta sigma weight residual 114.37 116.36 -1.99 1.26e+00 6.30e-01 2.49e+00 ... (remaining 3508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 1328 16.38 - 32.75: 165 32.75 - 49.13: 53 49.13 - 65.50: 17 65.50 - 81.88: 4 Dihedral angle restraints: 1567 sinusoidal: 636 harmonic: 931 Sorted by residual: dihedral pdb=" C5' GDP B 201 " pdb=" O5' GDP B 201 " pdb=" PA GDP B 201 " pdb=" O3A GDP B 201 " ideal model delta sinusoidal sigma weight residual 179.98 -124.68 -55.34 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CB LYS B 16 " pdb=" CG LYS B 16 " pdb=" CD LYS B 16 " pdb=" CE LYS B 16 " ideal model delta sinusoidal sigma weight residual -60.00 -115.98 55.98 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CB LYS B 5 " pdb=" CG LYS B 5 " pdb=" CD LYS B 5 " pdb=" CE LYS B 5 " ideal model delta sinusoidal sigma weight residual 60.00 115.02 -55.02 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 1564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 226 0.022 - 0.045: 94 0.045 - 0.067: 44 0.067 - 0.089: 14 0.089 - 0.111: 21 Chirality restraints: 399 Sorted by residual: chirality pdb=" CA VAL B 8 " pdb=" N VAL B 8 " pdb=" C VAL B 8 " pdb=" CB VAL B 8 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.09e-01 chirality pdb=" CA VAL B 125 " pdb=" N VAL B 125 " pdb=" C VAL B 125 " pdb=" CB VAL B 125 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.96e-01 chirality pdb=" CA VAL B 45 " pdb=" N VAL B 45 " pdb=" C VAL B 45 " pdb=" CB VAL B 45 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.89e-01 ... (remaining 396 not shown) Planarity restraints: 457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 235 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO A 236 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 268 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO A 269 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 202 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 203 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.017 5.00e-02 4.00e+02 ... (remaining 454 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 23 2.52 - 3.12: 1798 3.12 - 3.71: 3773 3.71 - 4.31: 5532 4.31 - 4.90: 9394 Nonbonded interactions: 20520 Sorted by model distance: nonbonded pdb="MG MG B 202 " pdb=" O HOH B 302 " model vdw 1.926 2.170 nonbonded pdb=" OG SER B 17 " pdb="MG MG B 202 " model vdw 1.930 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 303 " model vdw 1.934 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 301 " model vdw 1.948 2.170 nonbonded pdb=" O3B GDP B 201 " pdb="MG MG B 202 " model vdw 2.014 2.170 ... (remaining 20515 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.640 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2596 Z= 0.108 Angle : 0.478 6.285 3513 Z= 0.244 Chirality : 0.037 0.111 399 Planarity : 0.004 0.039 457 Dihedral : 16.941 81.879 967 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.87 % Allowed : 20.90 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.45), residues: 319 helix: 0.33 (0.37), residues: 174 sheet: 0.89 (0.82), residues: 44 loop : -0.69 (0.56), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.006 0.001 TYR B 40 PHE 0.005 0.001 PHE B 28 TRP 0.001 0.000 TRP A 255 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 2596) covalent geometry : angle 0.47812 ( 3513) hydrogen bonds : bond 0.26104 ( 130) hydrogen bonds : angle 7.43805 ( 384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8714 (tptp) cc_final: 0.7027 (mptt) REVERT: A 165 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7646 (mm-30) REVERT: A 221 LYS cc_start: 0.8001 (mttt) cc_final: 0.7456 (mtpt) REVERT: B 95 HIS cc_start: 0.7333 (m-70) cc_final: 0.7058 (m90) REVERT: B 111 MET cc_start: 0.8408 (ttm) cc_final: 0.8134 (mtp) outliers start: 5 outliers final: 6 residues processed: 76 average time/residue: 0.6039 time to fit residues: 46.8495 Evaluate side-chains 60 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 301 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.0070 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 227 ASN B 95 HIS B 99 GLN B 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.137012 restraints weight = 3133.427| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.15 r_work: 0.3424 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2596 Z= 0.109 Angle : 0.535 10.776 3513 Z= 0.254 Chirality : 0.038 0.117 399 Planarity : 0.004 0.036 457 Dihedral : 6.753 54.669 370 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.10 % Allowed : 19.78 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.44), residues: 319 helix: 1.20 (0.35), residues: 178 sheet: 0.85 (0.79), residues: 44 loop : -0.38 (0.62), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 123 TYR 0.008 0.001 TYR B 40 PHE 0.006 0.001 PHE B 90 TRP 0.005 0.001 TRP A 255 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 2596) covalent geometry : angle 0.53541 ( 3513) hydrogen bonds : bond 0.03839 ( 130) hydrogen bonds : angle 4.85144 ( 384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.6815 (mptt) REVERT: A 221 LYS cc_start: 0.8091 (mttt) cc_final: 0.7634 (mtpt) REVERT: B 30 ASP cc_start: 0.8655 (t0) cc_final: 0.7921 (m-30) REVERT: B 73 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7819 (mtm110) REVERT: B 126 ASP cc_start: 0.5666 (t0) cc_final: 0.5365 (t70) outliers start: 11 outliers final: 2 residues processed: 66 average time/residue: 0.6008 time to fit residues: 40.3714 Evaluate side-chains 52 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 283 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 18 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.168177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138268 restraints weight = 3146.231| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.22 r_work: 0.3519 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 2596 Z= 0.100 Angle : 0.515 10.767 3513 Z= 0.238 Chirality : 0.038 0.114 399 Planarity : 0.004 0.038 457 Dihedral : 5.270 53.321 360 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.48 % Allowed : 22.01 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.45), residues: 319 helix: 1.72 (0.36), residues: 178 sheet: 0.82 (0.78), residues: 44 loop : -0.32 (0.62), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 254 TYR 0.007 0.001 TYR B 96 PHE 0.005 0.001 PHE B 90 TRP 0.002 0.001 TRP A 255 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 2596) covalent geometry : angle 0.51534 ( 3513) hydrogen bonds : bond 0.03338 ( 130) hydrogen bonds : angle 4.45535 ( 384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 221 LYS cc_start: 0.8061 (mttt) cc_final: 0.7607 (mtpt) REVERT: B 70 GLN cc_start: 0.8341 (tt0) cc_final: 0.7937 (tt0) REVERT: B 111 MET cc_start: 0.8426 (ttm) cc_final: 0.8065 (mtp) outliers start: 12 outliers final: 2 residues processed: 57 average time/residue: 0.6191 time to fit residues: 36.0057 Evaluate side-chains 51 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.165990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137559 restraints weight = 3128.374| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.94 r_work: 0.3505 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 2596 Z= 0.130 Angle : 0.558 11.580 3513 Z= 0.255 Chirality : 0.040 0.117 399 Planarity : 0.004 0.036 457 Dihedral : 5.580 54.385 360 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 7.09 % Allowed : 19.78 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.45), residues: 319 helix: 1.74 (0.36), residues: 178 sheet: 0.73 (0.77), residues: 44 loop : -0.34 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 254 TYR 0.008 0.001 TYR B 40 PHE 0.005 0.001 PHE A 298 TRP 0.002 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 2596) covalent geometry : angle 0.55785 ( 3513) hydrogen bonds : bond 0.03606 ( 130) hydrogen bonds : angle 4.48577 ( 384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7126 (mptt) REVERT: A 221 LYS cc_start: 0.8081 (mttt) cc_final: 0.7613 (mtpt) REVERT: B 70 GLN cc_start: 0.8313 (tt0) cc_final: 0.7960 (tt0) REVERT: B 111 MET cc_start: 0.8452 (ttm) cc_final: 0.8144 (mtp) outliers start: 19 outliers final: 7 residues processed: 58 average time/residue: 0.5705 time to fit residues: 33.8310 Evaluate side-chains 55 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 154 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.165592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137233 restraints weight = 3125.956| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.93 r_work: 0.3504 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 2596 Z= 0.129 Angle : 0.556 12.203 3513 Z= 0.258 Chirality : 0.040 0.117 399 Planarity : 0.004 0.038 457 Dihedral : 5.629 56.676 360 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.10 % Allowed : 22.76 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.45), residues: 319 helix: 1.84 (0.36), residues: 178 sheet: 0.73 (0.79), residues: 43 loop : -0.18 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.008 0.001 TYR B 40 PHE 0.005 0.001 PHE A 298 TRP 0.002 0.001 TRP A 255 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2596) covalent geometry : angle 0.55646 ( 3513) hydrogen bonds : bond 0.03450 ( 130) hydrogen bonds : angle 4.40737 ( 384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7127 (mptt) REVERT: A 221 LYS cc_start: 0.8095 (mttt) cc_final: 0.7625 (mtpt) REVERT: B 70 GLN cc_start: 0.8283 (tt0) cc_final: 0.7881 (tt0) REVERT: B 111 MET cc_start: 0.8454 (ttm) cc_final: 0.8124 (mtp) outliers start: 11 outliers final: 6 residues processed: 58 average time/residue: 0.5944 time to fit residues: 35.2574 Evaluate side-chains 54 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 154 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.163260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.134599 restraints weight = 3151.885| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.93 r_work: 0.3473 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 2596 Z= 0.191 Angle : 0.618 12.678 3513 Z= 0.291 Chirality : 0.042 0.131 399 Planarity : 0.005 0.041 457 Dihedral : 6.092 59.947 360 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.85 % Allowed : 21.64 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.45), residues: 319 helix: 1.60 (0.36), residues: 178 sheet: 0.69 (0.81), residues: 43 loop : -0.53 (0.59), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 243 TYR 0.011 0.002 TYR B 96 PHE 0.007 0.001 PHE A 298 TRP 0.005 0.002 TRP A 255 HIS 0.005 0.002 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 2596) covalent geometry : angle 0.61782 ( 3513) hydrogen bonds : bond 0.04229 ( 130) hydrogen bonds : angle 4.63961 ( 384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7146 (mptt) REVERT: B 70 GLN cc_start: 0.8293 (tt0) cc_final: 0.7919 (tt0) outliers start: 13 outliers final: 7 residues processed: 54 average time/residue: 0.5334 time to fit residues: 29.4587 Evaluate side-chains 48 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 162 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.166147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137500 restraints weight = 3089.383| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.92 r_work: 0.3503 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 2596 Z= 0.129 Angle : 0.575 12.590 3513 Z= 0.270 Chirality : 0.039 0.115 399 Planarity : 0.004 0.040 457 Dihedral : 5.694 57.133 360 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.36 % Allowed : 23.88 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.45), residues: 319 helix: 1.83 (0.36), residues: 178 sheet: 0.50 (0.80), residues: 43 loop : -0.29 (0.60), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.007 0.001 TYR B 40 PHE 0.005 0.001 PHE B 156 TRP 0.002 0.001 TRP A 255 HIS 0.007 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2596) covalent geometry : angle 0.57458 ( 3513) hydrogen bonds : bond 0.03336 ( 130) hydrogen bonds : angle 4.37048 ( 384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7127 (mptt) REVERT: B 70 GLN cc_start: 0.8299 (tt0) cc_final: 0.7925 (tt0) REVERT: B 111 MET cc_start: 0.8380 (ttm) cc_final: 0.8039 (mtp) outliers start: 9 outliers final: 5 residues processed: 49 average time/residue: 0.5528 time to fit residues: 27.7261 Evaluate side-chains 49 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 154 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.165782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136664 restraints weight = 3164.682| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.00 r_work: 0.3500 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 2596 Z= 0.135 Angle : 0.574 12.566 3513 Z= 0.269 Chirality : 0.039 0.115 399 Planarity : 0.004 0.040 457 Dihedral : 5.748 57.900 360 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.99 % Allowed : 23.13 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.41 (0.45), residues: 319 helix: 1.77 (0.36), residues: 178 sheet: 0.45 (0.78), residues: 44 loop : -0.33 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 97 TYR 0.009 0.001 TYR B 96 PHE 0.005 0.001 PHE A 298 TRP 0.002 0.001 TRP A 255 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 2596) covalent geometry : angle 0.57445 ( 3513) hydrogen bonds : bond 0.03435 ( 130) hydrogen bonds : angle 4.39724 ( 384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7134 (mptt) REVERT: B 70 GLN cc_start: 0.8290 (tt0) cc_final: 0.7904 (tt0) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.5569 time to fit residues: 27.3695 Evaluate side-chains 49 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 154 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.166032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136592 restraints weight = 3223.969| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.03 r_work: 0.3496 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 2596 Z= 0.140 Angle : 0.592 12.711 3513 Z= 0.276 Chirality : 0.040 0.116 399 Planarity : 0.005 0.040 457 Dihedral : 5.803 58.283 360 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.73 % Allowed : 23.13 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.45), residues: 319 helix: 1.77 (0.36), residues: 178 sheet: 0.47 (0.79), residues: 43 loop : -0.35 (0.60), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 73 TYR 0.012 0.001 TYR B 96 PHE 0.005 0.001 PHE A 298 TRP 0.002 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2596) covalent geometry : angle 0.59198 ( 3513) hydrogen bonds : bond 0.03423 ( 130) hydrogen bonds : angle 4.40556 ( 384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7168 (mptt) REVERT: B 70 GLN cc_start: 0.8229 (tt0) cc_final: 0.7869 (tt0) REVERT: B 95 HIS cc_start: 0.7186 (m-70) cc_final: 0.6860 (m90) REVERT: B 111 MET cc_start: 0.8350 (ttm) cc_final: 0.8145 (ttm) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.5791 time to fit residues: 28.3931 Evaluate side-chains 48 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 154 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.166191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136619 restraints weight = 3152.634| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.03 r_work: 0.3486 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 2596 Z= 0.141 Angle : 0.588 12.638 3513 Z= 0.276 Chirality : 0.039 0.116 399 Planarity : 0.005 0.040 457 Dihedral : 5.769 58.368 360 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.99 % Allowed : 23.51 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.45), residues: 319 helix: 1.76 (0.36), residues: 178 sheet: 0.45 (0.80), residues: 43 loop : -0.38 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 73 TYR 0.012 0.001 TYR B 96 PHE 0.005 0.001 PHE A 298 TRP 0.002 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 2596) covalent geometry : angle 0.58795 ( 3513) hydrogen bonds : bond 0.03428 ( 130) hydrogen bonds : angle 4.40760 ( 384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7184 (mptt) REVERT: B 70 GLN cc_start: 0.8223 (tt0) cc_final: 0.7859 (tt0) REVERT: B 95 HIS cc_start: 0.7176 (m-70) cc_final: 0.6851 (m90) REVERT: B 111 MET cc_start: 0.8352 (ttm) cc_final: 0.8144 (ttm) outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 0.6036 time to fit residues: 29.0142 Evaluate side-chains 49 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 154 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.166965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137511 restraints weight = 3163.758| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.00 r_work: 0.3497 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 2596 Z= 0.122 Angle : 0.599 12.698 3513 Z= 0.277 Chirality : 0.040 0.157 399 Planarity : 0.004 0.040 457 Dihedral : 5.767 57.783 360 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.36 % Allowed : 22.76 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.46), residues: 319 helix: 1.86 (0.36), residues: 178 sheet: 0.38 (0.81), residues: 42 loop : -0.21 (0.62), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 73 TYR 0.011 0.001 TYR B 96 PHE 0.004 0.001 PHE B 90 TRP 0.001 0.001 TRP A 255 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 2596) covalent geometry : angle 0.59897 ( 3513) hydrogen bonds : bond 0.03167 ( 130) hydrogen bonds : angle 4.32858 ( 384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1335.00 seconds wall clock time: 23 minutes 29.57 seconds (1409.57 seconds total)