Starting phenix.real_space_refine on Thu Jul 2 18:18:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k2z_62001/07_2026/9k2z_62001.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k2z_62001/07_2026/9k2z_62001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k2z_62001/07_2026/9k2z_62001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k2z_62001/07_2026/9k2z_62001.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k2z_62001/07_2026/9k2z_62001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k2z_62001/07_2026/9k2z_62001.map" } resolution = 2.78 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= -0.007 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 347 5.49 5 Mg 4 5.21 5 S 7 5.16 5 C 4728 2.51 5 N 1756 2.21 5 O 2754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9596 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2203 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 252} Chain breaks: 2 Chain: "B" Number of atoms: 6670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 6670 Classifications: {'RNA': 313} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 18, 'rna3p_pur': 155, 'rna3p_pyr': 122} Link IDs: {'rna2p': 35, 'rna3p': 277} Chain breaks: 2 Chain: "C" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4, 'water': 17} Link IDs: {None: 20} Time building chain proxies: 2.13, per 1000 atoms: 0.22 Number of scatterers: 9596 At special positions: 0 Unit cell: (77.8125, 118.275, 161.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 7 16.00 P 347 15.00 Mg 4 11.99 O 2754 8.00 N 1756 7.00 C 4728 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: 0.79 Conformation dependent library (CDL) restraints added in 115.5 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 498 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 3 sheets defined 25.2% alpha, 26.3% beta 128 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 132 through 150 removed outlier: 3.585A pdb=" N LYS A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.554A pdb=" N GLU A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.031A pdb=" N VAL A 40 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 158 removed outlier: 6.556A pdb=" N GLN A 74 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 82 " --> pdb=" O GLN A 74 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N TRP A 329 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS A 85 " --> pdb=" O TRP A 329 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE A 331 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A 87 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLU A 89 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 390 through 391 removed outlier: 7.079A pdb=" N ALA A 377 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU A 371 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN A 379 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP A 352 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER A 355 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 397 " --> pdb=" O SER A 355 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 552 hydrogen bond angles 0 basepair planarities 128 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1210 1.33 - 1.45: 4570 1.45 - 1.57: 4017 1.57 - 1.69: 694 1.69 - 1.81: 10 Bond restraints: 10501 Sorted by residual: bond pdb=" P A B 34 " pdb=" OP2 A B 34 " ideal model delta sigma weight residual 1.485 1.645 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" C4 C B 151 " pdb=" C5 C B 151 " ideal model delta sigma weight residual 1.425 1.386 0.039 8.00e-03 1.56e+04 2.34e+01 bond pdb=" P A B 34 " pdb=" OP1 A B 34 " ideal model delta sigma weight residual 1.485 1.581 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C4 C B 117 " pdb=" C5 C B 117 " ideal model delta sigma weight residual 1.425 1.394 0.031 8.00e-03 1.56e+04 1.53e+01 bond pdb=" C4 C B 148 " pdb=" N4 C B 148 " ideal model delta sigma weight residual 1.335 1.303 0.032 9.00e-03 1.23e+04 1.30e+01 ... (remaining 10496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 13660 2.06 - 4.12: 2002 4.12 - 6.17: 161 6.17 - 8.23: 23 8.23 - 10.29: 2 Bond angle restraints: 15848 Sorted by residual: angle pdb=" O2' G B 253 " pdb=" C2' G B 253 " pdb=" C1' G B 253 " ideal model delta sigma weight residual 108.40 116.95 -8.55 1.50e+00 4.44e-01 3.25e+01 angle pdb=" C LYS A 388 " pdb=" CA LYS A 388 " pdb=" CB LYS A 388 " ideal model delta sigma weight residual 110.42 120.71 -10.29 1.99e+00 2.53e-01 2.67e+01 angle pdb=" O4' DT C 7 " pdb=" C4' DT C 7 " pdb=" C3' DT C 7 " ideal model delta sigma weight residual 106.00 102.93 3.07 6.00e-01 2.78e+00 2.62e+01 angle pdb=" C4' A B 284 " pdb=" C3' A B 284 " pdb=" O3' A B 284 " ideal model delta sigma weight residual 113.00 105.56 7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" CA ASP A 62 " pdb=" CB ASP A 62 " pdb=" CG ASP A 62 " ideal model delta sigma weight residual 112.60 117.39 -4.79 1.00e+00 1.00e+00 2.29e+01 ... (remaining 15843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 5256 19.50 - 39.00: 611 39.00 - 58.50: 310 58.50 - 78.00: 245 78.00 - 97.50: 4 Dihedral angle restraints: 6426 sinusoidal: 5652 harmonic: 774 Sorted by residual: dihedral pdb=" O4' A B 7 " pdb=" C1' A B 7 " pdb=" N9 A B 7 " pdb=" C4 A B 7 " ideal model delta sinusoidal sigma weight residual 68.00 148.96 -80.96 1 1.70e+01 3.46e-03 2.80e+01 dihedral pdb=" C LYS A 388 " pdb=" N LYS A 388 " pdb=" CA LYS A 388 " pdb=" CB LYS A 388 " ideal model delta harmonic sigma weight residual -122.60 -134.16 11.56 0 2.50e+00 1.60e-01 2.14e+01 dihedral pdb=" C5' G B 222 " pdb=" C4' G B 222 " pdb=" C3' G B 222 " pdb=" O3' G B 222 " ideal model delta sinusoidal sigma weight residual 82.00 112.43 -30.43 1 8.00e+00 1.56e-02 2.07e+01 ... (remaining 6423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 2003 0.214 - 0.429: 9 0.429 - 0.643: 2 0.643 - 0.858: 3 0.858 - 1.072: 1 Chirality restraints: 2018 Sorted by residual: chirality pdb=" P A B 34 " pdb=" OP1 A B 34 " pdb=" OP2 A B 34 " pdb=" O5' A B 34 " both_signs ideal model delta sigma weight residual True 2.41 3.48 -1.07 2.00e-01 2.50e+01 2.87e+01 chirality pdb=" P DG C 0 " pdb=" OP1 DG C 0 " pdb=" OP2 DG C 0 " pdb=" O5' DG C 0 " both_signs ideal model delta sigma weight residual True 2.34 2.99 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DG C -10 " pdb=" OP1 DG C -10 " pdb=" OP2 DG C -10 " pdb=" O5' DG C -10 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 2015 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 207 " -0.042 2.00e-02 2.50e+03 1.72e-02 8.92e+00 pdb=" N9 G B 207 " 0.032 2.00e-02 2.50e+03 pdb=" C8 G B 207 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G B 207 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 207 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G B 207 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G B 207 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G B 207 " -0.013 2.00e-02 2.50e+03 pdb=" C2 G B 207 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G B 207 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B 207 " 0.017 2.00e-02 2.50e+03 pdb=" C4 G B 207 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 115 " -0.041 2.00e-02 2.50e+03 1.89e-02 8.06e+00 pdb=" N1 U B 115 " 0.027 2.00e-02 2.50e+03 pdb=" C2 U B 115 " 0.012 2.00e-02 2.50e+03 pdb=" O2 U B 115 " 0.009 2.00e-02 2.50e+03 pdb=" N3 U B 115 " -0.006 2.00e-02 2.50e+03 pdb=" C4 U B 115 " -0.010 2.00e-02 2.50e+03 pdb=" O4 U B 115 " -0.013 2.00e-02 2.50e+03 pdb=" C5 U B 115 " 0.008 2.00e-02 2.50e+03 pdb=" C6 U B 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 175 " 0.039 2.00e-02 2.50e+03 1.63e-02 7.28e+00 pdb=" N9 A B 175 " -0.027 2.00e-02 2.50e+03 pdb=" C8 A B 175 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A B 175 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A B 175 " -0.008 2.00e-02 2.50e+03 pdb=" C6 A B 175 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A B 175 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A B 175 " 0.009 2.00e-02 2.50e+03 pdb=" C2 A B 175 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A B 175 " -0.012 2.00e-02 2.50e+03 pdb=" C4 A B 175 " -0.007 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 31 2.50 - 3.10: 5763 3.10 - 3.70: 17585 3.70 - 4.30: 26887 4.30 - 4.90: 34944 Nonbonded interactions: 85210 Sorted by model distance: nonbonded pdb=" OP1 U B 166 " pdb="MG MG B 404 " model vdw 1.898 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 504 " model vdw 2.006 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 508 " model vdw 2.020 2.170 nonbonded pdb="MG MG B 403 " pdb=" O HOH B 510 " model vdw 2.020 2.170 nonbonded pdb=" OP2 A B 146 " pdb="MG MG B 401 " model vdw 2.029 2.170 ... (remaining 85205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 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 : 0.011 0.160 10501 Z= 0.783 Angle : 1.404 10.291 15848 Z= 1.010 Chirality : 0.102 1.072 2018 Planarity : 0.006 0.057 725 Dihedral : 20.901 97.502 5928 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 11.11 % 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: -2.41 (0.47), residues: 256 helix: -0.94 (0.59), residues: 58 sheet: -1.23 (0.61), residues: 76 loop : -2.13 (0.46), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 122 TYR 0.015 0.002 TYR A 104 PHE 0.009 0.003 PHE A 380 TRP 0.009 0.003 TRP A 406 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.01072 / 0.78 (10501) covalent geometry : angle 1.40422 / 1.01 (15848) hydrogen bonds : bond 0.17741 / 11.49 ( 392) hydrogen bonds : angle 6.91651 / 4.84 ( 786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8343 (mmm160) cc_final: 0.8120 (mmm-85) REVERT: A 157 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7038 (mt-10) outliers start: 0 outliers final: 1 residues processed: 49 average time/residue: 0.8652 time to fit residues: 44.4445 Evaluate side-chains 33 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.107800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.069548 restraints weight = 21593.528| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.38 r_work: 0.2873 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10501 Z= 0.320 Angle : 0.613 9.550 15848 Z= 0.370 Chirality : 0.044 0.247 2018 Planarity : 0.006 0.043 725 Dihedral : 21.355 96.803 5350 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.27 % Allowed : 9.70 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.46 (0.51), residues: 256 helix: 1.12 (0.61), residues: 59 sheet: -1.73 (0.55), residues: 85 loop : -1.37 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 144 TYR 0.031 0.003 TYR A 356 PHE 0.014 0.002 PHE A 380 TRP 0.006 0.002 TRP A 399 HIS 0.015 0.003 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.32 (10501) covalent geometry : angle 0.61291 / 0.37 (15848) hydrogen bonds : bond 0.08053 / 5.39 ( 392) hydrogen bonds : angle 3.95034 / 2.91 ( 786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.174 Fit side-chains REVERT: A 50 ASP cc_start: 0.6965 (t0) cc_final: 0.6651 (t0) REVERT: A 56 ARG cc_start: 0.8554 (mmm160) cc_final: 0.8313 (mmm-85) REVERT: A 396 ARG cc_start: 0.8235 (ptt-90) cc_final: 0.7958 (ptt-90) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.6688 time to fit residues: 28.3811 Evaluate side-chains 30 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN A 11 ASN A 90 GLN A 379 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.105457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.065310 restraints weight = 20366.345| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.30 r_work: 0.2887 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10501 Z= 0.248 Angle : 0.500 6.733 15848 Z= 0.312 Chirality : 0.037 0.228 2018 Planarity : 0.005 0.036 725 Dihedral : 21.320 96.134 5348 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.53 % Allowed : 10.97 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.02 (0.53), residues: 256 helix: 1.88 (0.64), residues: 59 sheet: -1.57 (0.56), residues: 85 loop : -1.25 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 144 TYR 0.017 0.002 TYR A 405 PHE 0.015 0.002 PHE A 380 TRP 0.005 0.001 TRP A 399 HIS 0.006 0.002 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.25 (10501) covalent geometry : angle 0.50037 / 0.31 (15848) hydrogen bonds : bond 0.06437 / 4.32 ( 392) hydrogen bonds : angle 3.58920 / 2.67 ( 786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7066 (t0) cc_final: 0.6532 (t0) REVERT: A 56 ARG cc_start: 0.8617 (mmm160) cc_final: 0.8284 (mmm-85) REVERT: A 106 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8146 (mtt90) REVERT: A 396 ARG cc_start: 0.8278 (ptt-90) cc_final: 0.7998 (ptt-90) outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.8580 time to fit residues: 29.7459 Evaluate side-chains 36 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 57 optimal weight: 40.0000 chunk 56 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.104912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064674 restraints weight = 20448.415| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.41 r_work: 0.2873 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10501 Z= 0.297 Angle : 0.519 5.633 15848 Z= 0.319 Chirality : 0.039 0.233 2018 Planarity : 0.005 0.040 725 Dihedral : 21.292 95.639 5348 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.11 % Allowed : 12.66 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.02 (0.54), residues: 256 helix: 1.98 (0.64), residues: 59 sheet: -1.70 (0.54), residues: 85 loop : -1.21 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 113 TYR 0.028 0.002 TYR A 356 PHE 0.016 0.002 PHE A 380 TRP 0.007 0.002 TRP A 399 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.30 (10501) covalent geometry : angle 0.51875 / 0.32 (15848) hydrogen bonds : bond 0.06553 / 4.40 ( 392) hydrogen bonds : angle 3.55435 / 2.65 ( 786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8475 (mmm160) cc_final: 0.8183 (mmm-85) REVERT: A 106 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8223 (mtt90) REVERT: A 341 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7876 (pmtt) REVERT: A 396 ARG cc_start: 0.8240 (ptt-90) cc_final: 0.8022 (ptt-90) outliers start: 5 outliers final: 3 residues processed: 23 average time/residue: 1.2133 time to fit residues: 29.0391 Evaluate side-chains 27 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.108431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.070553 restraints weight = 21542.425| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.26 r_work: 0.2898 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10501 Z= 0.213 Angle : 0.462 4.524 15848 Z= 0.294 Chirality : 0.035 0.216 2018 Planarity : 0.005 0.039 725 Dihedral : 21.324 95.992 5348 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.11 % Allowed : 13.50 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.90 (0.54), residues: 256 helix: 2.29 (0.64), residues: 59 sheet: -1.73 (0.54), residues: 85 loop : -1.17 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 144 TYR 0.015 0.002 TYR A 405 PHE 0.012 0.002 PHE A 380 TRP 0.007 0.001 TRP A 399 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.21 (10501) covalent geometry : angle 0.46172 / 0.29 (15848) hydrogen bonds : bond 0.06136 / 4.13 ( 392) hydrogen bonds : angle 3.47276 / 2.59 ( 786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 396 ARG cc_start: 0.8232 (ptt-90) cc_final: 0.7984 (ptt-90) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 0.9937 time to fit residues: 22.7839 Evaluate side-chains 23 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 57 optimal weight: 40.0000 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 40.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.108956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.071179 restraints weight = 21631.582| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.24 r_work: 0.2923 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10501 Z= 0.180 Angle : 0.449 8.791 15848 Z= 0.286 Chirality : 0.033 0.207 2018 Planarity : 0.005 0.064 725 Dihedral : 21.296 96.681 5348 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.69 % Allowed : 14.35 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.83 (0.54), residues: 256 helix: 2.21 (0.67), residues: 58 sheet: -1.61 (0.55), residues: 85 loop : -1.06 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 56 TYR 0.015 0.002 TYR A 405 PHE 0.010 0.001 PHE A 380 TRP 0.006 0.001 TRP A 399 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.18 (10501) covalent geometry : angle 0.44949 / 0.29 (15848) hydrogen bonds : bond 0.05750 / 3.87 ( 392) hydrogen bonds : angle 3.43801 / 2.57 ( 786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7259 (tm-30) REVERT: A 284 GLU cc_start: 0.8279 (mp0) cc_final: 0.7688 (mp0) REVERT: A 396 ARG cc_start: 0.8223 (ptt-90) cc_final: 0.7880 (ptt-90) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 1.1205 time to fit residues: 26.8908 Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.105596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.065522 restraints weight = 20443.938| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.30 r_work: 0.2894 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10501 Z= 0.221 Angle : 0.462 7.413 15848 Z= 0.291 Chirality : 0.034 0.217 2018 Planarity : 0.005 0.045 725 Dihedral : 21.262 96.788 5348 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.53 % Allowed : 13.08 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.74 (0.54), residues: 256 helix: 2.38 (0.66), residues: 58 sheet: -1.55 (0.56), residues: 85 loop : -1.08 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 56 TYR 0.014 0.002 TYR A 405 PHE 0.012 0.002 PHE A 380 TRP 0.006 0.001 TRP A 399 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.22 (10501) covalent geometry : angle 0.46247 / 0.29 (15848) hydrogen bonds : bond 0.05875 / 3.94 ( 392) hydrogen bonds : angle 3.43826 / 2.57 ( 786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8067 (mmm-85) REVERT: A 280 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6942 (tm-30) REVERT: A 284 GLU cc_start: 0.8004 (mp0) cc_final: 0.7375 (mp0) REVERT: A 396 ARG cc_start: 0.8236 (ptt-90) cc_final: 0.8002 (ptt-90) outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 1.0144 time to fit residues: 26.5082 Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.104587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064357 restraints weight = 20226.824| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.48 r_work: 0.2870 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10501 Z= 0.331 Angle : 0.539 7.153 15848 Z= 0.327 Chirality : 0.040 0.238 2018 Planarity : 0.005 0.039 725 Dihedral : 21.298 96.281 5348 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.69 % Allowed : 14.77 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.92 (0.54), residues: 256 helix: 2.15 (0.66), residues: 58 sheet: -1.63 (0.56), residues: 85 loop : -1.17 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 144 TYR 0.016 0.002 TYR A 405 PHE 0.018 0.003 PHE A 380 TRP 0.008 0.002 TRP A 399 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.33 (10501) covalent geometry : angle 0.53931 / 0.33 (15848) hydrogen bonds : bond 0.06612 / 4.41 ( 392) hydrogen bonds : angle 3.57347 / 2.68 ( 786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 284 GLU cc_start: 0.8180 (mp0) cc_final: 0.7552 (mp0) REVERT: A 396 ARG cc_start: 0.8207 (ptt-90) cc_final: 0.7981 (ptt-90) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.9145 time to fit residues: 21.9825 Evaluate side-chains 24 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.105667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065563 restraints weight = 20390.875| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.24 r_work: 0.2901 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10501 Z= 0.159 Angle : 0.465 6.855 15848 Z= 0.293 Chirality : 0.033 0.199 2018 Planarity : 0.005 0.041 725 Dihedral : 21.421 96.935 5348 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.27 % Allowed : 16.03 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.84 (0.54), residues: 256 helix: 2.32 (0.66), residues: 58 sheet: -1.70 (0.57), residues: 85 loop : -1.07 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 56 TYR 0.015 0.002 TYR A 405 PHE 0.010 0.002 PHE A 380 TRP 0.009 0.001 TRP A 399 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (10501) covalent geometry : angle 0.46499 / 0.29 (15848) hydrogen bonds : bond 0.06017 / 4.03 ( 392) hydrogen bonds : angle 3.48375 / 2.61 ( 786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8385 (mtp85) cc_final: 0.8107 (mmm-85) REVERT: A 280 GLU cc_start: 0.7478 (tm-30) cc_final: 0.6897 (tm-30) REVERT: A 284 GLU cc_start: 0.8195 (mp0) cc_final: 0.7502 (mp0) REVERT: A 396 ARG cc_start: 0.8244 (ptt-90) cc_final: 0.8033 (ptt-90) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 1.1320 time to fit residues: 25.9753 Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 30.0000 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.105021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.064824 restraints weight = 20278.960| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.35 r_work: 0.2879 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10501 Z= 0.281 Angle : 0.500 6.649 15848 Z= 0.308 Chirality : 0.037 0.234 2018 Planarity : 0.005 0.040 725 Dihedral : 21.318 96.841 5348 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.27 % Allowed : 16.03 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.85 (0.54), residues: 256 helix: 2.26 (0.66), residues: 58 sheet: -1.67 (0.57), residues: 85 loop : -1.09 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 144 TYR 0.014 0.002 TYR A 405 PHE 0.013 0.002 PHE A 380 TRP 0.008 0.002 TRP A 399 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.28 (10501) covalent geometry : angle 0.49988 / 0.31 (15848) hydrogen bonds : bond 0.06161 / 4.12 ( 392) hydrogen bonds : angle 3.49101 / 2.62 ( 786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8378 (mtp85) cc_final: 0.8110 (mmm-85) REVERT: A 280 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6882 (tm-30) REVERT: A 284 GLU cc_start: 0.8175 (mp0) cc_final: 0.7458 (mp0) REVERT: A 396 ARG cc_start: 0.8237 (ptt-90) cc_final: 0.8029 (ptt-90) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 1.0984 time to fit residues: 25.1983 Evaluate side-chains 24 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.105152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064961 restraints weight = 20250.330| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.32 r_work: 0.2884 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10501 Z= 0.234 Angle : 0.484 6.455 15848 Z= 0.301 Chirality : 0.035 0.218 2018 Planarity : 0.005 0.039 725 Dihedral : 21.326 96.929 5348 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.69 % Allowed : 15.19 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.84 (0.54), residues: 256 helix: 2.30 (0.66), residues: 58 sheet: -1.68 (0.57), residues: 85 loop : -1.09 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 56 TYR 0.015 0.002 TYR A 405 PHE 0.012 0.002 PHE A 380 TRP 0.007 0.001 TRP A 399 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.23 (10501) covalent geometry : angle 0.48449 / 0.30 (15848) hydrogen bonds : bond 0.06103 / 4.09 ( 392) hydrogen bonds : angle 3.48084 / 2.61 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3271.14 seconds wall clock time: 56 minutes 30.43 seconds (3390.43 seconds total)