Starting phenix.real_space_refine on Tue Feb 3 12:20:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8b_62167/02_2026/9k8b_62167.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8b_62167/02_2026/9k8b_62167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k8b_62167/02_2026/9k8b_62167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8b_62167/02_2026/9k8b_62167.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k8b_62167/02_2026/9k8b_62167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8b_62167/02_2026/9k8b_62167.map" } resolution = 3.06 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= 0.003 sd= 0.222 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 2 5.16 5 C 1132 2.51 5 N 293 2.21 5 O 336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 1765 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1763 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'TRANS': 218} 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: 0.59, per 1000 atoms: 0.33 Number of scatterers: 1765 At special positions: 0 Unit cell: (47.4012, 59.2515, 76.4883, 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 2 16.00 O 336 8.00 N 293 7.00 C 1132 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: 0.16 Conformation dependent library (CDL) restraints added in 71.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 58 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 166 " 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 416 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 84.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 7 through 24 Processing helix chain 'A' and resid 27 through 43 removed outlier: 4.004A pdb=" N ALA A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.887A pdb=" N ILE A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 94 through 113 Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.800A pdb=" N TYR A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 157 Processing helix chain 'A' and resid 160 through 179 removed outlier: 3.696A pdb=" N LYS A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 201 removed outlier: 4.349A pdb=" N MET A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 224 removed outlier: 3.613A pdb=" N ALA A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) 134 hydrogen bonds defined for protein. 402 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: 0.26 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 327 1.29 - 1.42: 331 1.42 - 1.54: 1112 1.54 - 1.67: 2 1.67 - 1.80: 4 Bond restraints: 1776 Sorted by residual: bond pdb=" C ARG A 153 " pdb=" O ARG A 153 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.16e-02 7.43e+03 3.89e+01 bond pdb=" CA LYS A 149 " pdb=" CB LYS A 149 " ideal model delta sigma weight residual 1.530 1.446 0.084 1.58e-02 4.01e+03 2.81e+01 bond pdb=" C LYS A 149 " pdb=" O LYS A 149 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.16e-02 7.43e+03 2.72e+01 bond pdb=" CA ASP A 105 " pdb=" C ASP A 105 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.35e-02 5.49e+03 2.33e+01 bond pdb=" C ASP A 105 " pdb=" O ASP A 105 " ideal model delta sigma weight residual 1.236 1.178 0.059 1.26e-02 6.30e+03 2.17e+01 ... (remaining 1771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 2176 1.23 - 2.46: 139 2.46 - 3.70: 29 3.70 - 4.93: 16 4.93 - 6.16: 4 Bond angle restraints: 2364 Sorted by residual: angle pdb=" N ILE A 88 " pdb=" CA ILE A 88 " pdb=" C ILE A 88 " ideal model delta sigma weight residual 112.29 107.77 4.52 9.40e-01 1.13e+00 2.32e+01 angle pdb=" CA LYS A 149 " pdb=" C LYS A 149 " pdb=" N GLU A 150 " ideal model delta sigma weight residual 116.79 122.95 -6.16 1.28e+00 6.10e-01 2.32e+01 angle pdb=" O LYS A 152 " pdb=" C LYS A 152 " pdb=" N ARG A 153 " ideal model delta sigma weight residual 122.07 117.20 4.87 1.03e+00 9.43e-01 2.24e+01 angle pdb=" CA ARG A 153 " pdb=" C ARG A 153 " pdb=" N LEU A 154 " ideal model delta sigma weight residual 116.79 122.20 -5.41 1.28e+00 6.10e-01 1.79e+01 angle pdb=" O PHE A 148 " pdb=" C PHE A 148 " pdb=" N LYS A 149 " ideal model delta sigma weight residual 122.07 117.76 4.31 1.03e+00 9.43e-01 1.75e+01 ... (remaining 2359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 900 17.59 - 35.18: 161 35.18 - 52.77: 57 52.77 - 70.36: 9 70.36 - 87.95: 6 Dihedral angle restraints: 1133 sinusoidal: 495 harmonic: 638 Sorted by residual: dihedral pdb=" N MET A 6 " pdb=" C MET A 6 " pdb=" CA MET A 6 " pdb=" CB MET A 6 " ideal model delta harmonic sigma weight residual 122.80 133.23 -10.43 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" CA ASP A 131 " pdb=" CB ASP A 131 " pdb=" CG ASP A 131 " pdb=" OD1 ASP A 131 " ideal model delta sinusoidal sigma weight residual -30.00 -87.56 57.56 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU A 11 " pdb=" CG GLU A 11 " pdb=" CD GLU A 11 " pdb=" OE1 GLU A 11 " ideal model delta sinusoidal sigma weight residual 0.00 -87.95 87.95 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 1130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 271 0.132 - 0.264: 2 0.264 - 0.396: 0 0.396 - 0.528: 0 0.528 - 0.660: 1 Chirality restraints: 274 Sorted by residual: chirality pdb=" CA MET A 6 " pdb=" N MET A 6 " pdb=" C MET A 6 " pdb=" CB MET A 6 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA LYS A 149 " pdb=" N LYS A 149 " pdb=" C LYS A 149 " pdb=" CB LYS A 149 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ASP A 105 " pdb=" N ASP A 105 " pdb=" C ASP A 105 " pdb=" CB ASP A 105 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 271 not shown) Planarity restraints: 295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 148 " 0.015 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C PHE A 148 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE A 148 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS A 149 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 152 " 0.010 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C LYS A 152 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS A 152 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 153 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 153 " -0.009 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C ARG A 153 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG A 153 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 154 " -0.010 2.00e-02 2.50e+03 ... (remaining 292 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 6 2.54 - 3.13: 1258 3.13 - 3.72: 2662 3.72 - 4.31: 3598 4.31 - 4.90: 6341 Nonbonded interactions: 13865 Sorted by model distance: nonbonded pdb=" OD1 ASP A 32 " pdb="ZN ZN A 301 " model vdw 1.955 2.230 nonbonded pdb=" OD2 ASP A 162 " pdb="ZN ZN A 302 " model vdw 1.984 2.230 nonbonded pdb=" OD1 ASP A 32 " pdb=" NE2 HIS A 58 " model vdw 2.430 3.120 nonbonded pdb=" OE1 GLU A 67 " pdb=" NZ LYS A 69 " model vdw 2.441 3.120 nonbonded pdb=" OH TYR A 79 " pdb=" OD2 ASP A 105 " model vdw 2.447 3.040 ... (remaining 13860 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: 1.050 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.140 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.009 0.198 1778 Z= 0.468 Angle : 0.791 6.159 2364 Z= 0.556 Chirality : 0.057 0.660 274 Planarity : 0.003 0.028 295 Dihedral : 20.866 87.952 717 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.84 % Favored : 97.70 % Rotamer: Outliers : 1.08 % Allowed : 24.32 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.57), residues: 217 helix: 0.80 (0.38), residues: 192 sheet: None (None), residues: 0 loop : -2.93 (0.73), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.003 0.001 TYR A 79 PHE 0.008 0.002 PHE A 147 TRP 0.003 0.001 TRP A 151 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 1776) covalent geometry : angle 0.79113 ( 2364) hydrogen bonds : bond 0.10981 ( 134) hydrogen bonds : angle 4.52231 ( 402) metal coordination : bond 0.19342 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.095 Fit side-chains REVERT: A 149 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6809 (mmtt) outliers start: 2 outliers final: 0 residues processed: 17 average time/residue: 0.1397 time to fit residues: 2.6531 Evaluate side-chains 16 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.191245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.166853 restraints weight = 1455.622| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.12 r_work: 0.3750 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1778 Z= 0.112 Angle : 0.421 3.100 2364 Z= 0.249 Chirality : 0.031 0.089 274 Planarity : 0.002 0.019 295 Dihedral : 4.794 23.694 236 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.46 % Allowed : 0.92 % Favored : 98.62 % Rotamer: Outliers : 2.16 % Allowed : 23.24 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.58), residues: 217 helix: 1.44 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -2.63 (0.75), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.002 0.001 TYR A 118 PHE 0.003 0.001 PHE A 147 TRP 0.005 0.001 TRP A 151 HIS 0.001 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 1776) covalent geometry : angle 0.42078 ( 2364) hydrogen bonds : bond 0.03868 ( 134) hydrogen bonds : angle 3.53212 ( 402) metal coordination : bond 0.00238 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.070 Fit side-chains REVERT: A 17 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: A 29 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.5874 (m-30) REVERT: A 71 GLU cc_start: 0.8640 (tt0) cc_final: 0.8203 (pt0) REVERT: A 177 GLU cc_start: 0.7489 (tt0) cc_final: 0.7046 (tt0) outliers start: 4 outliers final: 2 residues processed: 20 average time/residue: 0.0850 time to fit residues: 1.9596 Evaluate side-chains 18 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 0.0050 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.171560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141691 restraints weight = 1585.138| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.42 r_work: 0.3477 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1778 Z= 0.118 Angle : 0.400 3.165 2364 Z= 0.235 Chirality : 0.030 0.090 274 Planarity : 0.002 0.016 295 Dihedral : 4.217 12.514 232 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.46 % Allowed : 0.92 % Favored : 98.62 % Rotamer: Outliers : 2.70 % Allowed : 24.86 % Favored : 72.43 % 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: 1.79 (0.57), residues: 217 helix: 1.68 (0.38), residues: 191 sheet: None (None), residues: 0 loop : -2.50 (0.82), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.003 0.001 TYR A 118 PHE 0.005 0.001 PHE A 147 TRP 0.004 0.001 TRP A 151 HIS 0.001 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 1776) covalent geometry : angle 0.39969 ( 2364) hydrogen bonds : bond 0.03999 ( 134) hydrogen bonds : angle 3.40783 ( 402) metal coordination : bond 0.00133 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.069 Fit side-chains REVERT: A 17 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: A 29 ASP cc_start: 0.6543 (OUTLIER) cc_final: 0.5860 (m-30) REVERT: A 71 GLU cc_start: 0.8726 (tt0) cc_final: 0.8207 (pt0) REVERT: A 177 GLU cc_start: 0.7377 (tt0) cc_final: 0.6971 (tt0) outliers start: 5 outliers final: 3 residues processed: 24 average time/residue: 0.1017 time to fit residues: 2.7449 Evaluate side-chains 21 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.170423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140925 restraints weight = 1555.245| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.39 r_work: 0.3477 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1778 Z= 0.122 Angle : 0.401 3.181 2364 Z= 0.233 Chirality : 0.031 0.091 274 Planarity : 0.002 0.014 295 Dihedral : 4.155 12.060 232 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.84 % Favored : 97.70 % Rotamer: Outliers : 3.24 % Allowed : 25.41 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.57), residues: 217 helix: 1.76 (0.38), residues: 191 sheet: None (None), residues: 0 loop : -2.53 (0.81), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.003 0.001 TYR A 118 PHE 0.005 0.001 PHE A 147 TRP 0.004 0.001 TRP A 151 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 1776) covalent geometry : angle 0.40059 ( 2364) hydrogen bonds : bond 0.03996 ( 134) hydrogen bonds : angle 3.37672 ( 402) metal coordination : bond 0.00116 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.071 Fit side-chains REVERT: A 17 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: A 29 ASP cc_start: 0.6383 (OUTLIER) cc_final: 0.5708 (m-30) REVERT: A 71 GLU cc_start: 0.8721 (tt0) cc_final: 0.8220 (pt0) REVERT: A 177 GLU cc_start: 0.7343 (tt0) cc_final: 0.6973 (tt0) REVERT: A 219 LYS cc_start: 0.7107 (mmtp) cc_final: 0.5990 (ttpt) outliers start: 6 outliers final: 3 residues processed: 22 average time/residue: 0.0920 time to fit residues: 2.3022 Evaluate side-chains 20 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.170370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141147 restraints weight = 1562.607| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.38 r_work: 0.3577 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1778 Z= 0.125 Angle : 0.404 3.190 2364 Z= 0.233 Chirality : 0.031 0.092 274 Planarity : 0.002 0.015 295 Dihedral : 4.117 11.887 232 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.38 % Favored : 98.16 % Rotamer: Outliers : 3.78 % Allowed : 25.41 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.57), residues: 217 helix: 1.80 (0.38), residues: 191 sheet: None (None), residues: 0 loop : -2.58 (0.78), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.003 0.001 TYR A 118 PHE 0.005 0.001 PHE A 147 TRP 0.005 0.001 TRP A 151 HIS 0.002 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 1776) covalent geometry : angle 0.40426 ( 2364) hydrogen bonds : bond 0.04064 ( 134) hydrogen bonds : angle 3.36889 ( 402) metal coordination : bond 0.00143 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.064 Fit side-chains REVERT: A 17 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: A 29 ASP cc_start: 0.6373 (OUTLIER) cc_final: 0.5698 (m-30) REVERT: A 71 GLU cc_start: 0.8782 (tt0) cc_final: 0.8296 (pt0) REVERT: A 177 GLU cc_start: 0.7442 (tt0) cc_final: 0.7102 (tt0) REVERT: A 219 LYS cc_start: 0.7148 (mmtp) cc_final: 0.6059 (ttpt) outliers start: 7 outliers final: 4 residues processed: 23 average time/residue: 0.0824 time to fit residues: 2.1214 Evaluate side-chains 21 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 3 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.177762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151177 restraints weight = 1556.107| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.28 r_work: 0.3525 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1778 Z= 0.102 Angle : 0.370 3.413 2364 Z= 0.216 Chirality : 0.030 0.088 274 Planarity : 0.002 0.013 295 Dihedral : 3.903 10.929 232 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.38 % Favored : 98.16 % Rotamer: Outliers : 3.78 % Allowed : 25.41 % Favored : 70.81 % 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: 2.24 (0.57), residues: 217 helix: 2.01 (0.38), residues: 191 sheet: None (None), residues: 0 loop : -2.59 (0.74), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.002 0.001 TYR A 118 PHE 0.003 0.001 PHE A 147 TRP 0.005 0.001 TRP A 151 HIS 0.001 0.000 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 1776) covalent geometry : angle 0.37014 ( 2364) hydrogen bonds : bond 0.03552 ( 134) hydrogen bonds : angle 3.23426 ( 402) metal coordination : bond 0.00087 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.072 Fit side-chains REVERT: A 17 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: A 29 ASP cc_start: 0.6410 (OUTLIER) cc_final: 0.5737 (m-30) REVERT: A 62 ASP cc_start: 0.7299 (t0) cc_final: 0.6034 (m-30) REVERT: A 71 GLU cc_start: 0.8737 (tt0) cc_final: 0.8277 (pt0) REVERT: A 142 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7261 (mp0) REVERT: A 177 GLU cc_start: 0.7451 (tt0) cc_final: 0.7096 (tt0) REVERT: A 219 LYS cc_start: 0.7134 (mmtp) cc_final: 0.6042 (ttpt) outliers start: 7 outliers final: 5 residues processed: 22 average time/residue: 0.0916 time to fit residues: 2.2870 Evaluate side-chains 23 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140887 restraints weight = 1549.918| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.52 r_work: 0.3504 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1778 Z= 0.124 Angle : 0.405 3.499 2364 Z= 0.230 Chirality : 0.031 0.093 274 Planarity : 0.002 0.014 295 Dihedral : 4.007 11.897 232 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.38 % Favored : 98.16 % Rotamer: Outliers : 4.86 % Allowed : 23.78 % Favored : 71.35 % 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: 2.14 (0.56), residues: 217 helix: 1.94 (0.37), residues: 191 sheet: None (None), residues: 0 loop : -2.62 (0.70), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.003 0.001 TYR A 118 PHE 0.004 0.001 PHE A 147 TRP 0.005 0.001 TRP A 151 HIS 0.002 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 1776) covalent geometry : angle 0.40548 ( 2364) hydrogen bonds : bond 0.04052 ( 134) hydrogen bonds : angle 3.31057 ( 402) metal coordination : bond 0.00122 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.071 Fit side-chains REVERT: A 17 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: A 29 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5544 (m-30) REVERT: A 71 GLU cc_start: 0.8592 (tt0) cc_final: 0.8190 (pt0) REVERT: A 156 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5507 (ptpt) REVERT: A 177 GLU cc_start: 0.7271 (tt0) cc_final: 0.6909 (tt0) REVERT: A 219 LYS cc_start: 0.7076 (mmtp) cc_final: 0.5983 (ttpt) outliers start: 9 outliers final: 5 residues processed: 27 average time/residue: 0.0878 time to fit residues: 2.6756 Evaluate side-chains 26 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.0070 chunk 12 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.171384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140860 restraints weight = 1569.186| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.55 r_work: 0.3587 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1778 Z= 0.109 Angle : 0.406 5.240 2364 Z= 0.228 Chirality : 0.030 0.091 274 Planarity : 0.002 0.014 295 Dihedral : 3.887 11.405 232 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.86 % Allowed : 24.86 % Favored : 70.27 % 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: 2.25 (0.56), residues: 217 helix: 2.00 (0.37), residues: 192 sheet: None (None), residues: 0 loop : -2.74 (0.68), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.002 0.001 TYR A 118 PHE 0.003 0.001 PHE A 147 TRP 0.005 0.001 TRP A 151 HIS 0.001 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 1776) covalent geometry : angle 0.40559 ( 2364) hydrogen bonds : bond 0.03698 ( 134) hydrogen bonds : angle 3.21570 ( 402) metal coordination : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 0.047 Fit side-chains REVERT: A 17 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 29 ASP cc_start: 0.6103 (OUTLIER) cc_final: 0.5492 (m-30) REVERT: A 71 GLU cc_start: 0.8604 (tt0) cc_final: 0.8199 (pt0) REVERT: A 142 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7090 (mp0) REVERT: A 156 LYS cc_start: 0.5965 (OUTLIER) cc_final: 0.5484 (ptpt) REVERT: A 177 GLU cc_start: 0.7255 (tt0) cc_final: 0.6888 (tt0) REVERT: A 219 LYS cc_start: 0.7089 (mmtp) cc_final: 0.6003 (ttpt) outliers start: 9 outliers final: 5 residues processed: 25 average time/residue: 0.0551 time to fit residues: 1.5659 Evaluate side-chains 24 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.169303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138796 restraints weight = 1575.302| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.56 r_work: 0.3507 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1778 Z= 0.131 Angle : 0.431 5.236 2364 Z= 0.240 Chirality : 0.032 0.095 274 Planarity : 0.002 0.013 295 Dihedral : 4.005 12.543 232 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.32 % Allowed : 25.95 % Favored : 69.73 % 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: 2.09 (0.56), residues: 217 helix: 1.89 (0.37), residues: 192 sheet: None (None), residues: 0 loop : -2.67 (0.67), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.004 0.001 TYR A 79 PHE 0.004 0.001 PHE A 147 TRP 0.004 0.001 TRP A 151 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 1776) covalent geometry : angle 0.43102 ( 2364) hydrogen bonds : bond 0.04152 ( 134) hydrogen bonds : angle 3.30425 ( 402) metal coordination : bond 0.00138 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.070 Fit side-chains REVERT: A 17 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: A 29 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5557 (m-30) REVERT: A 52 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7898 (mp0) REVERT: A 71 GLU cc_start: 0.8570 (tt0) cc_final: 0.8148 (pt0) REVERT: A 156 LYS cc_start: 0.6003 (OUTLIER) cc_final: 0.5514 (ptpt) REVERT: A 177 GLU cc_start: 0.7300 (tt0) cc_final: 0.6906 (tt0) REVERT: A 219 LYS cc_start: 0.7165 (mmtp) cc_final: 0.6080 (ttpt) outliers start: 8 outliers final: 5 residues processed: 24 average time/residue: 0.0913 time to fit residues: 2.4815 Evaluate side-chains 25 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 4 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.171135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142306 restraints weight = 1554.293| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.39 r_work: 0.3612 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1778 Z= 0.127 Angle : 0.455 6.627 2364 Z= 0.247 Chirality : 0.031 0.105 274 Planarity : 0.002 0.013 295 Dihedral : 3.992 12.513 232 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.32 % Allowed : 27.03 % Favored : 68.65 % 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: 2.12 (0.56), residues: 217 helix: 1.90 (0.37), residues: 192 sheet: None (None), residues: 0 loop : -2.62 (0.68), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.003 0.001 TYR A 79 PHE 0.004 0.001 PHE A 168 TRP 0.004 0.001 TRP A 151 HIS 0.002 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 1776) covalent geometry : angle 0.45527 ( 2364) hydrogen bonds : bond 0.04016 ( 134) hydrogen bonds : angle 3.29877 ( 402) metal coordination : bond 0.00132 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.043 Fit side-chains REVERT: A 17 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: A 29 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.5662 (m-30) REVERT: A 71 GLU cc_start: 0.8776 (tt0) cc_final: 0.8248 (pt0) REVERT: A 156 LYS cc_start: 0.6077 (OUTLIER) cc_final: 0.5588 (ptpt) REVERT: A 177 GLU cc_start: 0.7483 (tt0) cc_final: 0.7109 (tt0) REVERT: A 219 LYS cc_start: 0.7254 (mmtp) cc_final: 0.6160 (ttpt) outliers start: 8 outliers final: 5 residues processed: 23 average time/residue: 0.0566 time to fit residues: 1.4745 Evaluate side-chains 23 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 15 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.0030 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.176382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148209 restraints weight = 1578.272| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.38 r_work: 0.3618 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1778 Z= 0.104 Angle : 0.425 7.473 2364 Z= 0.232 Chirality : 0.031 0.126 274 Planarity : 0.002 0.013 295 Dihedral : 3.797 10.966 232 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.38 % Favored : 98.16 % Rotamer: Outliers : 4.32 % Allowed : 25.95 % Favored : 69.73 % 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: 2.40 (0.56), residues: 217 helix: 2.17 (0.37), residues: 190 sheet: None (None), residues: 0 loop : -2.85 (0.65), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.002 0.001 TYR A 118 PHE 0.003 0.001 PHE A 117 TRP 0.006 0.001 TRP A 151 HIS 0.001 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 1776) covalent geometry : angle 0.42479 ( 2364) hydrogen bonds : bond 0.03523 ( 134) hydrogen bonds : angle 3.19765 ( 402) metal coordination : bond 0.00090 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 684.99 seconds wall clock time: 12 minutes 17.92 seconds (737.92 seconds total)