Starting phenix.real_space_refine on Tue Feb 3 12:20:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8f_62171/02_2026/9k8f_62171.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8f_62171/02_2026/9k8f_62171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k8f_62171/02_2026/9k8f_62171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8f_62171/02_2026/9k8f_62171.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k8f_62171/02_2026/9k8f_62171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8f_62171/02_2026/9k8f_62171.map" } resolution = 2.75 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= 0.002 sd= 0.232 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 Zn 2 6.06 5 S 6 5.16 5 C 1187 2.51 5 N 298 2.21 5 O 342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1835 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1833 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 1, 'TRANS': 226} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.54, per 1000 atoms: 0.29 Number of scatterers: 1835 At special positions: 0 Unit cell: (74.3337, 58.1742, 49.5558, 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) Zn 2 29.99 S 6 16.00 O 342 8.00 N 298 7.00 C 1187 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: 0.18 Conformation dependent library (CDL) restraints added in 106.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 47 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 195 " 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 434 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 removed outlier: 3.600A pdb=" N ALA A 10 " --> pdb=" O MET A 6 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 41 Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.602A pdb=" N LEU A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 93 through 112 removed outlier: 3.782A pdb=" N LYS A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 138 removed outlier: 3.956A pdb=" N LYS A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 164 removed outlier: 3.875A pdb=" N LYS A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 Processing helix chain 'A' and resid 191 through 210 Processing helix chain 'A' and resid 213 through 231 removed outlier: 4.388A pdb=" N LYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) 152 hydrogen bonds defined for protein. 456 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: 0.28 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 603 1.35 - 1.46: 326 1.46 - 1.58: 908 1.58 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 1849 Sorted by residual: bond pdb=" CB GLU A 7 " pdb=" CG GLU A 7 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.91e-01 bond pdb=" CG MET A 125 " pdb=" SD MET A 125 " ideal model delta sigma weight residual 1.803 1.786 0.017 2.50e-02 1.60e+03 4.79e-01 bond pdb=" CB GLU A 143 " pdb=" CG GLU A 143 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.48e-01 bond pdb=" CA GLU A 220 " pdb=" CB GLU A 220 " ideal model delta sigma weight residual 1.528 1.539 -0.010 1.56e-02 4.11e+03 4.30e-01 bond pdb=" CG1 ILE A 163 " pdb=" CD1 ILE A 163 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.16e-01 ... (remaining 1844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 2428 1.46 - 2.93: 34 2.93 - 4.39: 8 4.39 - 5.86: 0 5.86 - 7.32: 2 Bond angle restraints: 2472 Sorted by residual: angle pdb=" CB MET A 96 " pdb=" CG MET A 96 " pdb=" SD MET A 96 " ideal model delta sigma weight residual 112.70 120.02 -7.32 3.00e+00 1.11e-01 5.96e+00 angle pdb=" CA GLU A 220 " pdb=" CB GLU A 220 " pdb=" CG GLU A 220 " ideal model delta sigma weight residual 114.10 118.35 -4.25 2.00e+00 2.50e-01 4.51e+00 angle pdb=" CB GLU A 7 " pdb=" CG GLU A 7 " pdb=" CD GLU A 7 " ideal model delta sigma weight residual 112.60 115.87 -3.27 1.70e+00 3.46e-01 3.69e+00 angle pdb=" N ASN A 92 " pdb=" CA ASN A 92 " pdb=" C ASN A 92 " ideal model delta sigma weight residual 108.58 111.94 -3.36 1.82e+00 3.02e-01 3.41e+00 angle pdb=" C LEU A 91 " pdb=" N ASN A 92 " pdb=" CA ASN A 92 " ideal model delta sigma weight residual 122.32 119.40 2.92 1.63e+00 3.76e-01 3.21e+00 ... (remaining 2467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 906 15.47 - 30.94: 147 30.94 - 46.41: 79 46.41 - 61.87: 26 61.87 - 77.34: 6 Dihedral angle restraints: 1164 sinusoidal: 499 harmonic: 665 Sorted by residual: dihedral pdb=" CG ARG A 11 " pdb=" CD ARG A 11 " pdb=" NE ARG A 11 " pdb=" CZ ARG A 11 " ideal model delta sinusoidal sigma weight residual 90.00 132.33 -42.33 2 1.50e+01 4.44e-03 9.67e+00 dihedral pdb=" CG ARG A 66 " pdb=" CD ARG A 66 " pdb=" NE ARG A 66 " pdb=" CZ ARG A 66 " ideal model delta sinusoidal sigma weight residual 90.00 47.98 42.02 2 1.50e+01 4.44e-03 9.56e+00 dihedral pdb=" CA ARG A 198 " pdb=" CB ARG A 198 " pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " ideal model delta sinusoidal sigma weight residual -60.00 -119.75 59.75 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 166 0.022 - 0.044: 85 0.044 - 0.067: 24 0.067 - 0.089: 17 0.089 - 0.111: 2 Chirality restraints: 294 Sorted by residual: chirality pdb=" CA GLU A 220 " pdb=" N GLU A 220 " pdb=" C GLU A 220 " pdb=" CB GLU A 220 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.07e-01 chirality pdb=" CA PRO A 94 " pdb=" N PRO A 94 " pdb=" C PRO A 94 " pdb=" CB PRO A 94 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.68e-01 chirality pdb=" CA MET A 125 " pdb=" N MET A 125 " pdb=" C MET A 125 " pdb=" CB MET A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.43 0.08 2.00e-01 2.50e+01 1.59e-01 ... (remaining 291 not shown) Planarity restraints: 309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 66 " 0.091 9.50e-02 1.11e+02 4.09e-02 1.29e+00 pdb=" NE ARG A 66 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 66 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 66 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 66 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 220 " 0.004 2.00e-02 2.50e+03 8.46e-03 7.15e-01 pdb=" CD GLU A 220 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLU A 220 " 0.005 2.00e-02 2.50e+03 pdb=" OE2 GLU A 220 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 143 " 0.003 2.00e-02 2.50e+03 6.51e-03 4.23e-01 pdb=" CD GLU A 143 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLU A 143 " 0.004 2.00e-02 2.50e+03 pdb=" OE2 GLU A 143 " 0.004 2.00e-02 2.50e+03 ... (remaining 306 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 11 2.57 - 3.15: 1348 3.15 - 3.73: 2957 3.73 - 4.32: 3930 4.32 - 4.90: 6569 Nonbonded interactions: 14815 Sorted by model distance: nonbonded pdb=" OD2 ASP A 191 " pdb="ZN ZN A 302 " model vdw 1.985 2.230 nonbonded pdb=" OD2 ASP A 51 " pdb="ZN ZN A 301 " model vdw 2.178 2.230 nonbonded pdb=" OD1 ASP A 51 " pdb="ZN ZN A 301 " model vdw 2.261 2.230 nonbonded pdb=" OE1 GLU A 8 " pdb=" OH TYR A 41 " model vdw 2.290 3.040 nonbonded pdb=" NZ LYS A 85 " pdb=" OE1 GLU A 104 " model vdw 2.312 3.120 ... (remaining 14810 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.210 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.006 0.214 1851 Z= 0.220 Angle : 0.501 7.322 2472 Z= 0.267 Chirality : 0.032 0.111 294 Planarity : 0.003 0.041 309 Dihedral : 20.806 77.342 730 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 2.06 % Allowed : 34.54 % Favored : 63.40 % 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: 3.17 (0.52), residues: 226 helix: 2.58 (0.34), residues: 199 sheet: None (None), residues: 0 loop : -1.93 (0.87), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 66 TYR 0.005 0.001 TYR A 107 PHE 0.004 0.001 PHE A 88 HIS 0.003 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 1849) covalent geometry : angle 0.50065 ( 2472) hydrogen bonds : bond 0.14405 ( 152) hydrogen bonds : angle 4.08902 ( 456) metal coordination : bond 0.15691 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.080 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 28 average time/residue: 0.9110 time to fit residues: 25.8430 Evaluate side-chains 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 230 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.174282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145075 restraints weight = 1580.220| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.18 r_work: 0.3607 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1851 Z= 0.119 Angle : 0.431 5.066 2472 Z= 0.223 Chirality : 0.031 0.094 294 Planarity : 0.003 0.028 309 Dihedral : 5.900 48.907 249 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.09 % Allowed : 30.93 % Favored : 65.98 % 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: 3.44 (0.53), residues: 226 helix: 2.56 (0.34), residues: 207 sheet: None (None), residues: 0 loop : -1.34 (1.35), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 66 TYR 0.007 0.001 TYR A 41 PHE 0.002 0.001 PHE A 88 HIS 0.004 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 1849) covalent geometry : angle 0.43137 ( 2472) hydrogen bonds : bond 0.04463 ( 152) hydrogen bonds : angle 3.32570 ( 456) metal coordination : bond 0.00156 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.075 Fit side-chains REVERT: A 8 GLU cc_start: 0.8284 (tt0) cc_final: 0.8047 (tt0) REVERT: A 15 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7127 (mmm160) REVERT: A 93 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 98 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7173 (mtmt) REVERT: A 223 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6686 (pt0) outliers start: 6 outliers final: 2 residues processed: 34 average time/residue: 1.0223 time to fit residues: 35.1384 Evaluate side-chains 32 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 230 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.172146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142317 restraints weight = 1565.800| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.18 r_work: 0.3590 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1851 Z= 0.127 Angle : 0.427 5.307 2472 Z= 0.221 Chirality : 0.032 0.099 294 Planarity : 0.003 0.032 309 Dihedral : 4.292 36.497 243 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.09 % Allowed : 30.93 % Favored : 65.98 % 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: 3.37 (0.52), residues: 226 helix: 2.52 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -1.33 (1.34), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 66 TYR 0.006 0.001 TYR A 41 PHE 0.004 0.001 PHE A 88 HIS 0.004 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 1849) covalent geometry : angle 0.42684 ( 2472) hydrogen bonds : bond 0.04633 ( 152) hydrogen bonds : angle 3.28725 ( 456) metal coordination : bond 0.00097 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.077 Fit side-chains REVERT: A 8 GLU cc_start: 0.8227 (tt0) cc_final: 0.8012 (tt0) REVERT: A 15 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7127 (mmm160) REVERT: A 98 LYS cc_start: 0.8059 (tmtt) cc_final: 0.7214 (mtmt) REVERT: A 124 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7761 (mt-10) outliers start: 6 outliers final: 3 residues processed: 32 average time/residue: 1.0580 time to fit residues: 34.2433 Evaluate side-chains 30 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 230 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.0570 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.172619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143250 restraints weight = 1518.849| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.14 r_work: 0.3609 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1851 Z= 0.118 Angle : 0.421 5.781 2472 Z= 0.216 Chirality : 0.031 0.095 294 Planarity : 0.002 0.014 309 Dihedral : 3.904 24.939 243 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.61 % Allowed : 31.96 % Favored : 64.43 % 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: 3.55 (0.52), residues: 226 helix: 2.64 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -1.35 (1.34), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.005 0.001 TYR A 107 PHE 0.003 0.001 PHE A 88 HIS 0.004 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 1849) covalent geometry : angle 0.42072 ( 2472) hydrogen bonds : bond 0.04319 ( 152) hydrogen bonds : angle 3.21135 ( 456) metal coordination : bond 0.00086 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.077 Fit side-chains REVERT: A 8 GLU cc_start: 0.8258 (tt0) cc_final: 0.8019 (tt0) REVERT: A 9 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7687 (tp) REVERT: A 98 LYS cc_start: 0.8025 (tmtt) cc_final: 0.7218 (mtmt) REVERT: A 124 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7703 (mt-10) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 0.9627 time to fit residues: 34.1136 Evaluate side-chains 30 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 167 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.170912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141282 restraints weight = 1495.694| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.15 r_work: 0.3589 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1851 Z= 0.136 Angle : 0.452 5.727 2472 Z= 0.232 Chirality : 0.032 0.100 294 Planarity : 0.002 0.016 309 Dihedral : 3.577 18.175 241 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.12 % Allowed : 31.44 % Favored : 64.43 % 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: 3.53 (0.52), residues: 226 helix: 2.64 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -1.46 (1.34), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 109 TYR 0.005 0.001 TYR A 41 PHE 0.004 0.001 PHE A 88 HIS 0.004 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 1849) covalent geometry : angle 0.45185 ( 2472) hydrogen bonds : bond 0.04702 ( 152) hydrogen bonds : angle 3.25086 ( 456) metal coordination : bond 0.00158 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.076 Fit side-chains REVERT: A 8 GLU cc_start: 0.8185 (tt0) cc_final: 0.7956 (tt0) REVERT: A 9 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7677 (tp) REVERT: A 15 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7109 (mmm160) REVERT: A 98 LYS cc_start: 0.8054 (tmtt) cc_final: 0.7208 (mtmm) REVERT: A 117 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 124 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7716 (mt-10) outliers start: 8 outliers final: 2 residues processed: 35 average time/residue: 0.9977 time to fit residues: 35.2944 Evaluate side-chains 32 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 167 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 10 optimal weight: 0.0970 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.173524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144276 restraints weight = 1498.496| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.16 r_work: 0.3626 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1851 Z= 0.104 Angle : 0.407 6.002 2472 Z= 0.208 Chirality : 0.030 0.092 294 Planarity : 0.002 0.011 309 Dihedral : 3.463 17.804 241 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.12 % Allowed : 30.93 % Favored : 64.95 % 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: 3.85 (0.52), residues: 226 helix: 2.84 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -1.30 (1.35), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.004 0.001 TYR A 107 PHE 0.003 0.001 PHE A 219 HIS 0.004 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 1849) covalent geometry : angle 0.40734 ( 2472) hydrogen bonds : bond 0.03790 ( 152) hydrogen bonds : angle 3.09468 ( 456) metal coordination : bond 0.00079 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.045 Fit side-chains REVERT: A 8 GLU cc_start: 0.8217 (tt0) cc_final: 0.7980 (tt0) REVERT: A 9 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7621 (tp) REVERT: A 15 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7103 (mmm160) REVERT: A 93 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: A 98 LYS cc_start: 0.7999 (tmtt) cc_final: 0.7136 (mtmt) REVERT: A 117 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 124 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 183 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7226 (mt-10) outliers start: 8 outliers final: 2 residues processed: 32 average time/residue: 0.8413 time to fit residues: 27.2128 Evaluate side-chains 32 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 167 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 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 = 0.3873 r_free = 0.3873 target = 0.171925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142579 restraints weight = 1487.197| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.15 r_work: 0.3607 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1851 Z= 0.121 Angle : 0.448 6.938 2472 Z= 0.227 Chirality : 0.031 0.096 294 Planarity : 0.002 0.014 309 Dihedral : 3.480 18.320 241 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.61 % Allowed : 31.96 % Favored : 64.43 % 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: 3.80 (0.52), residues: 226 helix: 2.81 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -1.32 (1.37), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.006 0.001 TYR A 107 PHE 0.003 0.001 PHE A 88 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 1849) covalent geometry : angle 0.44764 ( 2472) hydrogen bonds : bond 0.04238 ( 152) hydrogen bonds : angle 3.14867 ( 456) metal coordination : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.044 Fit side-chains REVERT: A 8 GLU cc_start: 0.8165 (tt0) cc_final: 0.7914 (tt0) REVERT: A 9 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7617 (tp) REVERT: A 15 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7102 (mmm160) REVERT: A 98 LYS cc_start: 0.8009 (tmtt) cc_final: 0.7209 (mtmt) REVERT: A 117 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: A 124 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7656 (mt-10) outliers start: 7 outliers final: 2 residues processed: 31 average time/residue: 0.6323 time to fit residues: 19.8440 Evaluate side-chains 30 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 167 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.172778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.143007 restraints weight = 1524.308| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.19 r_work: 0.3570 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1851 Z= 0.113 Angle : 0.435 7.157 2472 Z= 0.220 Chirality : 0.031 0.095 294 Planarity : 0.002 0.012 309 Dihedral : 3.468 18.451 241 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.12 % Allowed : 31.44 % Favored : 64.43 % 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: 3.88 (0.52), residues: 226 helix: 2.86 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -1.29 (1.36), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.006 0.001 TYR A 107 PHE 0.003 0.001 PHE A 88 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 1849) covalent geometry : angle 0.43477 ( 2472) hydrogen bonds : bond 0.04028 ( 152) hydrogen bonds : angle 3.12365 ( 456) metal coordination : bond 0.00110 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.044 Fit side-chains REVERT: A 8 GLU cc_start: 0.8219 (tt0) cc_final: 0.7956 (tt0) REVERT: A 9 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7624 (tp) REVERT: A 15 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7115 (mmm160) REVERT: A 93 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: A 98 LYS cc_start: 0.7979 (tmtt) cc_final: 0.7130 (mtmt) REVERT: A 107 TYR cc_start: 0.8045 (t80) cc_final: 0.7528 (t80) REVERT: A 117 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: A 124 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 183 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7236 (mt-10) outliers start: 8 outliers final: 2 residues processed: 32 average time/residue: 0.6432 time to fit residues: 20.8137 Evaluate side-chains 32 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 167 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 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 = 0.3863 r_free = 0.3863 target = 0.170572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139819 restraints weight = 1430.886| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.20 r_work: 0.3601 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1851 Z= 0.122 Angle : 0.468 8.145 2472 Z= 0.234 Chirality : 0.032 0.099 294 Planarity : 0.002 0.013 309 Dihedral : 3.473 18.486 241 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.12 % Allowed : 31.96 % Favored : 63.92 % 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 are not related in a simple way. whole: 3.83 (0.52), residues: 226 helix: 2.83 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -1.35 (1.35), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.006 0.001 TYR A 107 PHE 0.004 0.001 PHE A 88 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 1849) covalent geometry : angle 0.46801 ( 2472) hydrogen bonds : bond 0.04205 ( 152) hydrogen bonds : angle 3.14753 ( 456) metal coordination : bond 0.00118 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.044 Fit side-chains REVERT: A 8 GLU cc_start: 0.8274 (tt0) cc_final: 0.8018 (tt0) REVERT: A 9 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7572 (tp) REVERT: A 15 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7088 (mmm160) REVERT: A 98 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7172 (mtmt) REVERT: A 117 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 124 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7635 (mt-10) REVERT: A 183 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7197 (mt-10) REVERT: A 187 GLU cc_start: 0.7797 (tp30) cc_final: 0.6689 (pt0) outliers start: 8 outliers final: 3 residues processed: 33 average time/residue: 0.6418 time to fit residues: 21.4252 Evaluate side-chains 33 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 167 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.172134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142363 restraints weight = 1501.976| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.16 r_work: 0.3538 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1851 Z= 0.127 Angle : 0.472 8.370 2472 Z= 0.236 Chirality : 0.032 0.098 294 Planarity : 0.002 0.014 309 Dihedral : 3.501 18.673 241 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.61 % Allowed : 32.47 % Favored : 63.92 % 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 are not related in a simple way. whole: 3.75 (0.52), residues: 226 helix: 2.78 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -1.41 (1.33), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.006 0.001 TYR A 107 PHE 0.004 0.001 PHE A 88 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 1849) covalent geometry : angle 0.47204 ( 2472) hydrogen bonds : bond 0.04366 ( 152) hydrogen bonds : angle 3.18292 ( 456) metal coordination : bond 0.00135 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.043 Fit side-chains REVERT: A 8 GLU cc_start: 0.8172 (tt0) cc_final: 0.7912 (tt0) REVERT: A 9 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7568 (tp) REVERT: A 15 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7082 (mmm160) REVERT: A 98 LYS cc_start: 0.8029 (tmtt) cc_final: 0.7162 (mtmm) REVERT: A 117 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 124 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 183 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7340 (mt-10) REVERT: A 187 GLU cc_start: 0.7791 (tp30) cc_final: 0.6678 (pt0) outliers start: 7 outliers final: 3 residues processed: 33 average time/residue: 0.6923 time to fit residues: 23.0865 Evaluate side-chains 32 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 167 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.172128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142061 restraints weight = 1513.818| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.18 r_work: 0.3507 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1851 Z= 0.127 Angle : 0.475 8.375 2472 Z= 0.238 Chirality : 0.032 0.109 294 Planarity : 0.002 0.015 309 Dihedral : 3.498 18.741 241 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.61 % Allowed : 32.47 % Favored : 63.92 % 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 are not related in a simple way. whole: 3.71 (0.52), residues: 226 helix: 2.75 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -1.43 (1.34), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.005 0.001 TYR A 41 PHE 0.004 0.001 PHE A 88 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 1849) covalent geometry : angle 0.47451 ( 2472) hydrogen bonds : bond 0.04365 ( 152) hydrogen bonds : angle 3.19422 ( 456) metal coordination : bond 0.00140 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 927.64 seconds wall clock time: 16 minutes 21.87 seconds (981.87 seconds total)