Starting phenix.real_space_refine on Fri Aug 22 21:54:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2g_27835/08_2025/8e2g_27835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2g_27835/08_2025/8e2g_27835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e2g_27835/08_2025/8e2g_27835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2g_27835/08_2025/8e2g_27835.map" model { file = "/net/cci-nas-00/data/ceres_data/8e2g_27835/08_2025/8e2g_27835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2g_27835/08_2025/8e2g_27835.cif" } resolution = 2.99 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= -0.004 sd= 0.047 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2574 2.51 5 N 676 2.21 5 O 756 1.98 5 H 4078 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8110 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 8110 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 28, 'TRANS': 494} Chain breaks: 12 Time building chain proxies: 1.67, per 1000 atoms: 0.21 Number of scatterers: 8110 At special positions: 0 Unit cell: (70.4, 78.32, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 756 8.00 N 676 7.00 C 2574 6.00 H 4078 1.00 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: 0.70 Conformation dependent library (CDL) restraints added in 271.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 9 sheets defined 24.3% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 225 through 243 Processing helix chain 'A' and resid 247 through 263 removed outlier: 3.818A pdb=" N VAL A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.612A pdb=" N MET A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 removed outlier: 3.520A pdb=" N PHE A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.696A pdb=" N GLN A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 4.181A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 76 removed outlier: 3.880A pdb=" N ALA A 81 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 91 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 104 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 93 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 390 removed outlier: 6.464A pdb=" N ALA A 403 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 409 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 423 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 411 " --> pdb=" O HIS A 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 419 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 504 through 513 removed outlier: 5.553A pdb=" N LEU A 505 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 574 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE A 507 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 572 " --> pdb=" O ILE A 507 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS A 566 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 634 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 716 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 731 through 738 removed outlier: 6.709A pdb=" N GLY A 748 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A 736 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 746 " --> pdb=" O ILE A 736 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS A 744 " --> pdb=" O PRO A 738 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 902 through 903 removed outlier: 6.909A pdb=" N ILE A 914 " --> pdb=" O LEU A 923 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 940 through 945 removed outlier: 6.668A pdb=" N CYS A 955 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 943 " --> pdb=" O CYS A 953 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS A 953 " --> pdb=" O VAL A 943 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR A 945 " --> pdb=" O ARG A 951 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARG A 951 " --> pdb=" O TYR A 945 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4058 1.03 - 1.23: 22 1.23 - 1.42: 1641 1.42 - 1.62: 2432 1.62 - 1.81: 32 Bond restraints: 8185 Sorted by residual: bond pdb=" C ALA A 569 " pdb=" N GLY A 570 " ideal model delta sigma weight residual 1.331 1.319 0.012 6.60e-03 2.30e+04 3.19e+00 bond pdb=" CG1 ILE A 231 " pdb=" CD1 ILE A 231 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.31e-01 bond pdb=" CA ALA A 924 " pdb=" C ALA A 924 " ideal model delta sigma weight residual 1.529 1.521 0.008 1.04e-02 9.25e+03 5.74e-01 bond pdb=" CB ASP A 139 " pdb=" CG ASP A 139 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.24e-01 bond pdb=" N GLY A 748 " pdb=" CA GLY A 748 " ideal model delta sigma weight residual 1.456 1.447 0.008 1.16e-02 7.43e+03 4.80e-01 ... (remaining 8180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 14601 1.60 - 3.21: 211 3.21 - 4.81: 26 4.81 - 6.42: 1 6.42 - 8.02: 1 Bond angle restraints: 14840 Sorted by residual: angle pdb=" N ILE A 860 " pdb=" CA ILE A 860 " pdb=" C ILE A 860 " ideal model delta sigma weight residual 112.96 109.50 3.46 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA LEU A 861 " pdb=" CB LEU A 861 " pdb=" CG LEU A 861 " ideal model delta sigma weight residual 116.30 124.32 -8.02 3.50e+00 8.16e-02 5.25e+00 angle pdb=" CA ILE A 860 " pdb=" C ILE A 860 " pdb=" N LEU A 861 " ideal model delta sigma weight residual 118.65 116.61 2.04 1.07e+00 8.73e-01 3.64e+00 angle pdb=" N GLU A 343 " pdb=" CA GLU A 343 " pdb=" C GLU A 343 " ideal model delta sigma weight residual 110.14 107.38 2.76 1.51e+00 4.39e-01 3.35e+00 angle pdb=" C GLY A 570 " pdb=" N GLY A 571 " pdb=" CA GLY A 571 " ideal model delta sigma weight residual 121.58 120.04 1.54 8.60e-01 1.35e+00 3.20e+00 ... (remaining 14835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 3428 17.42 - 34.84: 296 34.84 - 52.25: 99 52.25 - 69.67: 25 69.67 - 87.09: 10 Dihedral angle restraints: 3858 sinusoidal: 2118 harmonic: 1740 Sorted by residual: dihedral pdb=" CA ILE A 914 " pdb=" C ILE A 914 " pdb=" N LEU A 915 " pdb=" CA LEU A 915 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASP A 430 " pdb=" CB ASP A 430 " pdb=" CG ASP A 430 " pdb=" OD1 ASP A 430 " ideal model delta sinusoidal sigma weight residual -30.00 -83.18 53.18 1 2.00e+01 2.50e-03 9.62e+00 dihedral pdb=" N LYS A 636 " pdb=" CA LYS A 636 " pdb=" CB LYS A 636 " pdb=" CG LYS A 636 " ideal model delta sinusoidal sigma weight residual -60.00 -116.64 56.64 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 342 0.027 - 0.053: 212 0.053 - 0.080: 50 0.080 - 0.106: 37 0.106 - 0.133: 24 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA ILE A 512 " pdb=" N ILE A 512 " pdb=" C ILE A 512 " pdb=" CB ILE A 512 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE A 914 " pdb=" N ILE A 914 " pdb=" C ILE A 914 " pdb=" CB ILE A 914 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 944 " pdb=" N ILE A 944 " pdb=" C ILE A 944 " pdb=" CB ILE A 944 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 662 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 430 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO A 431 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 627 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 628 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 737 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 738 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " 0.019 5.00e-02 4.00e+02 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 462 2.18 - 2.78: 16811 2.78 - 3.39: 23134 3.39 - 3.99: 30750 3.99 - 4.60: 47132 Nonbonded interactions: 118289 Sorted by model distance: nonbonded pdb=" O PRO A 929 " pdb=" H ASP A 938 " model vdw 1.572 2.450 nonbonded pdb=" OE1 GLN A 151 " pdb=" H GLN A 162 " model vdw 1.588 2.450 nonbonded pdb=" O GLU A 164 " pdb="HH22 ARG A 258 " model vdw 1.594 2.450 nonbonded pdb="HH12 ARG A 289 " pdb=" OD1 ASN A 365 " model vdw 1.598 2.450 nonbonded pdb=" H GLU A 339 " pdb=" OD2 ASP A 342 " model vdw 1.606 2.450 ... (remaining 118284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.270 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: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.780 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.003 0.033 4107 Z= 0.149 Angle : 0.603 8.023 5572 Z= 0.319 Chirality : 0.043 0.133 665 Planarity : 0.005 0.042 697 Dihedral : 15.682 87.087 1489 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.42 % Allowed : 19.78 % Favored : 77.80 % 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 aren not related in a simple way. whole: -1.77 (0.38), residues: 497 helix: -0.03 (0.48), residues: 120 sheet: -1.38 (0.47), residues: 135 loop : -1.59 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 750 TYR 0.007 0.001 TYR A 189 PHE 0.013 0.002 PHE A 192 TRP 0.006 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4107) covalent geometry : angle 0.60342 ( 5572) hydrogen bonds : bond 0.14907 ( 146) hydrogen bonds : angle 7.51883 ( 414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 57 average time/residue: 0.7583 time to fit residues: 45.4024 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 952 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.175427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.151455 restraints weight = 16933.951| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.17 r_work: 0.3872 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4107 Z= 0.162 Angle : 0.572 5.660 5572 Z= 0.295 Chirality : 0.044 0.150 665 Planarity : 0.005 0.045 697 Dihedral : 6.698 57.986 558 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.42 % Allowed : 18.90 % Favored : 78.68 % 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 aren not related in a simple way. whole: -1.92 (0.38), residues: 497 helix: -0.19 (0.45), residues: 129 sheet: -1.32 (0.45), residues: 139 loop : -1.81 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 289 TYR 0.007 0.001 TYR A 132 PHE 0.015 0.002 PHE A 192 TRP 0.006 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4107) covalent geometry : angle 0.57180 ( 5572) hydrogen bonds : bond 0.04328 ( 146) hydrogen bonds : angle 6.17938 ( 414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6330 (mp10) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 0.8013 time to fit residues: 46.1551 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 961 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.175485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.149377 restraints weight = 17006.268| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.00 r_work: 0.3895 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4107 Z= 0.150 Angle : 0.558 5.761 5572 Z= 0.285 Chirality : 0.043 0.146 665 Planarity : 0.004 0.045 697 Dihedral : 5.647 59.374 546 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.20 % Allowed : 20.00 % Favored : 77.80 % 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 aren not related in a simple way. whole: -1.84 (0.38), residues: 497 helix: -0.03 (0.46), residues: 129 sheet: -1.46 (0.44), residues: 141 loop : -1.69 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 387 TYR 0.008 0.001 TYR A 633 PHE 0.013 0.001 PHE A 192 TRP 0.006 0.001 TRP A 345 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4107) covalent geometry : angle 0.55816 ( 5572) hydrogen bonds : bond 0.03889 ( 146) hydrogen bonds : angle 5.87947 ( 414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6254 (mp10) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.8653 time to fit residues: 50.0166 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.175055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.147718 restraints weight = 17295.834| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.11 r_work: 0.3876 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4107 Z= 0.169 Angle : 0.574 5.264 5572 Z= 0.297 Chirality : 0.044 0.144 665 Planarity : 0.005 0.045 697 Dihedral : 5.685 56.931 546 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.65 % Favored : 91.15 % Rotamer: Outliers : 2.64 % Allowed : 20.00 % Favored : 77.36 % 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 aren not related in a simple way. whole: -1.81 (0.38), residues: 497 helix: -0.02 (0.46), residues: 129 sheet: -1.22 (0.47), residues: 124 loop : -1.81 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.009 0.001 TYR A 315 PHE 0.045 0.003 PHE A 920 TRP 0.007 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 4107) covalent geometry : angle 0.57383 ( 5572) hydrogen bonds : bond 0.03734 ( 146) hydrogen bonds : angle 5.79833 ( 414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 54 average time/residue: 0.8967 time to fit residues: 50.9036 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 961 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.176151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.149166 restraints weight = 17209.039| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.09 r_work: 0.3889 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4107 Z= 0.144 Angle : 0.553 5.629 5572 Z= 0.282 Chirality : 0.043 0.137 665 Planarity : 0.004 0.044 697 Dihedral : 5.548 55.040 546 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.42 % Allowed : 20.66 % Favored : 76.92 % 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 aren not related in a simple way. whole: -1.68 (0.38), residues: 497 helix: 0.20 (0.47), residues: 123 sheet: -1.27 (0.47), residues: 126 loop : -1.70 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 406 TYR 0.008 0.001 TYR A 315 PHE 0.018 0.002 PHE A 920 TRP 0.006 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4107) covalent geometry : angle 0.55258 ( 5572) hydrogen bonds : bond 0.03541 ( 146) hydrogen bonds : angle 5.66311 ( 414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.192 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.7776 time to fit residues: 43.3877 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.0020 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.176426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.149994 restraints weight = 16996.392| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.02 r_work: 0.3900 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4107 Z= 0.129 Angle : 0.538 5.419 5572 Z= 0.273 Chirality : 0.043 0.141 665 Planarity : 0.004 0.044 697 Dihedral : 5.358 52.975 546 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 1.76 % Allowed : 20.88 % Favored : 77.36 % 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 aren not related in a simple way. whole: -1.57 (0.38), residues: 497 helix: 0.35 (0.47), residues: 123 sheet: -1.19 (0.48), residues: 126 loop : -1.66 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 387 TYR 0.008 0.001 TYR A 315 PHE 0.013 0.002 PHE A 424 TRP 0.005 0.001 TRP A 345 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4107) covalent geometry : angle 0.53825 ( 5572) hydrogen bonds : bond 0.03340 ( 146) hydrogen bonds : angle 5.51693 ( 414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.6799 time to fit residues: 38.5385 Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.173537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.146692 restraints weight = 17432.914| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.08 r_work: 0.3859 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4107 Z= 0.232 Angle : 0.614 6.221 5572 Z= 0.317 Chirality : 0.045 0.140 665 Planarity : 0.005 0.044 697 Dihedral : 5.654 50.628 546 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 1.76 % Allowed : 21.54 % Favored : 76.70 % 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 aren not related in a simple way. whole: -1.89 (0.38), residues: 497 helix: -0.05 (0.46), residues: 123 sheet: -1.34 (0.48), residues: 126 loop : -1.80 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.013 0.002 TYR A 315 PHE 0.021 0.002 PHE A 192 TRP 0.010 0.002 TRP A 345 HIS 0.005 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 4107) covalent geometry : angle 0.61390 ( 5572) hydrogen bonds : bond 0.04076 ( 146) hydrogen bonds : angle 5.88687 ( 414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.222 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 52 average time/residue: 0.6874 time to fit residues: 37.7734 Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.175956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150457 restraints weight = 17023.067| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.95 r_work: 0.3909 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4107 Z= 0.107 Angle : 0.537 6.203 5572 Z= 0.270 Chirality : 0.043 0.139 665 Planarity : 0.004 0.047 697 Dihedral : 5.311 49.079 546 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.20 % Allowed : 21.32 % Favored : 76.48 % 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 aren not related in a simple way. whole: -1.54 (0.38), residues: 497 helix: 0.35 (0.48), residues: 123 sheet: -1.17 (0.49), residues: 126 loop : -1.64 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 387 TYR 0.007 0.001 TYR A 633 PHE 0.011 0.001 PHE A 725 TRP 0.004 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4107) covalent geometry : angle 0.53706 ( 5572) hydrogen bonds : bond 0.03148 ( 146) hydrogen bonds : angle 5.43344 ( 414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7884 (p) REVERT: A 942 SER cc_start: 0.8083 (m) cc_final: 0.7876 (m) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.6664 time to fit residues: 40.0984 Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.175402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.149670 restraints weight = 16961.451| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.95 r_work: 0.3907 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4107 Z= 0.133 Angle : 0.551 7.114 5572 Z= 0.278 Chirality : 0.043 0.131 665 Planarity : 0.004 0.045 697 Dihedral : 5.264 47.849 546 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.54 % Allowed : 22.42 % Favored : 76.04 % 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 aren not related in a simple way. whole: -1.55 (0.38), residues: 497 helix: 0.35 (0.48), residues: 123 sheet: -1.14 (0.49), residues: 126 loop : -1.67 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 387 TYR 0.008 0.001 TYR A 633 PHE 0.014 0.002 PHE A 424 TRP 0.004 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4107) covalent geometry : angle 0.55116 ( 5572) hydrogen bonds : bond 0.03301 ( 146) hydrogen bonds : angle 5.43358 ( 414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 SER cc_start: 0.8088 (m) cc_final: 0.7865 (m) outliers start: 7 outliers final: 7 residues processed: 53 average time/residue: 0.8144 time to fit residues: 45.2433 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.0670 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.176846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.150317 restraints weight = 17120.709| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.06 r_work: 0.3906 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4107 Z= 0.125 Angle : 0.547 7.117 5572 Z= 0.275 Chirality : 0.043 0.141 665 Planarity : 0.004 0.045 697 Dihedral : 5.196 47.091 546 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.54 % Allowed : 22.64 % Favored : 75.82 % 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 aren not related in a simple way. whole: -1.57 (0.38), residues: 497 helix: 0.36 (0.47), residues: 123 sheet: -1.17 (0.49), residues: 121 loop : -1.68 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 387 TYR 0.008 0.001 TYR A 633 PHE 0.012 0.001 PHE A 329 TRP 0.004 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4107) covalent geometry : angle 0.54674 ( 5572) hydrogen bonds : bond 0.03234 ( 146) hydrogen bonds : angle 5.36664 ( 414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 SER cc_start: 0.8139 (m) cc_final: 0.7908 (m) outliers start: 7 outliers final: 6 residues processed: 53 average time/residue: 0.7802 time to fit residues: 43.2745 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.176368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.150081 restraints weight = 17073.591| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.01 r_work: 0.3906 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4107 Z= 0.138 Angle : 0.556 6.988 5572 Z= 0.281 Chirality : 0.043 0.136 665 Planarity : 0.005 0.061 697 Dihedral : 5.210 45.652 546 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 1.10 % Allowed : 23.30 % Favored : 75.60 % 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 aren not related in a simple way. whole: -1.59 (0.38), residues: 497 helix: 0.35 (0.47), residues: 123 sheet: -1.18 (0.49), residues: 121 loop : -1.70 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 280 TYR 0.013 0.001 TYR A 315 PHE 0.014 0.002 PHE A 192 TRP 0.005 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4107) covalent geometry : angle 0.55581 ( 5572) hydrogen bonds : bond 0.03321 ( 146) hydrogen bonds : angle 5.39913 ( 414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3070.28 seconds wall clock time: 52 minutes 41.86 seconds (3161.86 seconds total)