Starting phenix.real_space_refine on Wed Aug 5 11:28:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k2z_62001/08_2026/9k2z_62001.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k2z_62001/08_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_62001/08_2026/9k2z_62001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k2z_62001/08_2026/9k2z_62001.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k2z_62001/08_2026/9k2z_62001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k2z_62001/08_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-2.2rc3-6140/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: 2.42, per 1000 atoms: 0.25 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: 1.03 Conformation dependent library (CDL) restraints added in 104.9 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: 1.76 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: 2.83 Time building geometry restraints manager: 1.35 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=" P A B 34 " pdb=" O5' A B 34 " ideal model delta sigma weight residual 1.593 1.629 -0.036 1.00e-02 1.00e+04 1.32e+01 ... (remaining 10496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 13996 2.06 - 4.12: 1696 4.12 - 6.17: 135 6.17 - 8.23: 20 8.23 - 10.29: 1 Bond angle restraints: 15848 Sorted by residual: angle pdb=" C2' A B 175 " pdb=" C1' A B 175 " pdb=" N9 A B 175 " ideal model delta sigma weight residual 112.00 117.86 -5.86 1.10e+00 8.26e-01 2.84e+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=" O4' C B 197 " pdb=" C1' C B 197 " pdb=" N1 C B 197 " ideal model delta sigma weight residual 108.50 112.07 -3.57 7.00e-01 2.04e+00 2.60e+01 angle pdb=" C2' G B 222 " pdb=" C1' G B 222 " pdb=" N9 G B 222 " ideal model delta sigma weight residual 112.00 117.57 -5.57 1.10e+00 8.26e-01 2.57e+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: 2006 0.214 - 0.429: 6 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: 1.900 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- 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= 0.823 Angle : 1.319 10.291 15848 Z= 0.990 Chirality : 0.089 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 0.01065 / 0.82 (10501) covalent geometry : angle 1.31950 / 0.99 (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 : 0.127 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: 0.8569 time to fit residues: 43.9235 Evaluate side-chains 34 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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: 8.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.107690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.069480 restraints weight = 21541.708| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.27 r_work: 0.2870 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10501 Z= 0.335 Angle : 0.705 10.406 15848 Z= 0.388 Chirality : 0.051 0.213 2018 Planarity : 0.006 0.040 725 Dihedral : 21.340 93.626 5350 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.27 % Allowed : 10.13 % Favored : 88.61 % 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: -1.48 (0.51), residues: 256 helix: 1.16 (0.61), residues: 59 sheet: -1.77 (0.54), residues: 85 loop : -1.40 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 144 TYR 0.032 0.003 TYR A 356 PHE 0.012 0.002 PHE A 380 TRP 0.007 0.002 TRP A 329 HIS 0.006 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.33 (10501) covalent geometry : angle 0.70546 / 0.39 (15848) hydrogen bonds : bond 0.08277 / 5.59 ( 392) hydrogen bonds : angle 3.95574 / 2.92 ( 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 : 0.170 Fit side-chains REVERT: A 50 ASP cc_start: 0.6973 (t0) cc_final: 0.6650 (t0) REVERT: A 56 ARG cc_start: 0.8567 (mmm160) cc_final: 0.8322 (mmm-85) REVERT: A 396 ARG cc_start: 0.8238 (ptt-90) cc_final: 0.7972 (ptt-90) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.6574 time to fit residues: 27.8896 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 : 0.159 ------------------------------------------------------------------------------- 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: 8.9990 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.104563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064401 restraints weight = 20292.236| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.28 r_work: 0.2868 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10501 Z= 0.299 Angle : 0.615 6.631 15848 Z= 0.346 Chirality : 0.044 0.183 2018 Planarity : 0.006 0.038 725 Dihedral : 21.298 93.040 5348 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -1.19 (0.53), residues: 256 helix: 1.62 (0.64), residues: 59 sheet: -1.60 (0.56), residues: 85 loop : -1.36 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 144 TYR 0.017 0.002 TYR A 405 PHE 0.019 0.002 PHE A 380 TRP 0.007 0.002 TRP A 329 HIS 0.008 0.002 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.30 (10501) covalent geometry : angle 0.61452 / 0.35 (15848) hydrogen bonds : bond 0.07123 / 4.75 ( 392) hydrogen bonds : angle 3.71981 / 2.76 ( 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 36 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7111 (t0) cc_final: 0.6613 (t0) REVERT: A 56 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8227 (mmm-85) REVERT: A 106 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8201 (mtt90) REVERT: A 396 ARG cc_start: 0.8257 (ptt-90) cc_final: 0.8044 (ptt-90) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.7656 time to fit residues: 26.5739 Evaluate side-chains 33 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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: 30.0000 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 57 optimal weight: 40.0000 chunk 56 optimal weight: 9.9990 overall best weight: 3.2384 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.104752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064573 restraints weight = 20441.360| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.27 r_work: 0.2875 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10501 Z= 0.283 Angle : 0.587 5.575 15848 Z= 0.333 Chirality : 0.042 0.186 2018 Planarity : 0.005 0.041 725 Dihedral : 21.300 92.964 5348 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.81 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: -1.09 (0.54), residues: 256 helix: 1.87 (0.64), residues: 59 sheet: -1.69 (0.54), residues: 85 loop : -1.25 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 144 TYR 0.027 0.002 TYR A 356 PHE 0.015 0.002 PHE A 380 TRP 0.008 0.002 TRP A 399 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.28 (10501) covalent geometry : angle 0.58717 / 0.33 (15848) hydrogen bonds : bond 0.06690 / 4.50 ( 392) hydrogen bonds : angle 3.60274 / 2.69 ( 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 : 0.176 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8508 (mmm160) cc_final: 0.8229 (mmm-85) REVERT: A 106 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8229 (mtt90) REVERT: A 396 ARG cc_start: 0.8255 (ptt-90) cc_final: 0.8013 (ptt-90) outliers start: 5 outliers final: 4 residues processed: 24 average time/residue: 1.0792 time to fit residues: 27.0600 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 : 0.108 ------------------------------------------------------------------------------- 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 128 SER 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: 0.6980 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 = 0.105274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.065182 restraints weight = 20389.065| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.24 r_work: 0.2893 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2329 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= 0.214 Angle : 0.525 4.763 15848 Z= 0.312 Chirality : 0.038 0.184 2018 Planarity : 0.005 0.042 725 Dihedral : 21.310 93.429 5348 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.53 % Allowed : 12.24 % 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: -0.96 (0.54), residues: 256 helix: 2.15 (0.64), residues: 59 sheet: -1.73 (0.54), residues: 85 loop : -1.18 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 144 TYR 0.016 0.002 TYR A 405 PHE 0.013 0.002 PHE A 380 TRP 0.008 0.001 TRP A 399 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.21 (10501) covalent geometry : angle 0.52541 / 0.31 (15848) hydrogen bonds : bond 0.06413 / 4.32 ( 392) hydrogen bonds : angle 3.53616 / 2.65 ( 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: 6 poor density : 20 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.5983 (OUTLIER) cc_final: 0.5779 (tt) REVERT: A 396 ARG cc_start: 0.8242 (ptt-90) cc_final: 0.8006 (ptt-90) outliers start: 6 outliers final: 3 residues processed: 23 average time/residue: 1.0520 time to fit residues: 25.2620 Evaluate side-chains 24 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 375 LEU 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: 6.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 57 optimal weight: 30.0000 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 29 optimal weight: 50.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.105465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065375 restraints weight = 20435.568| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.24 r_work: 0.2898 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2440 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= 0.215 Angle : 0.515 4.743 15848 Z= 0.306 Chirality : 0.038 0.179 2018 Planarity : 0.006 0.070 725 Dihedral : 21.287 94.129 5348 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.53 % Allowed : 14.35 % 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: -0.94 (0.54), residues: 256 helix: 1.93 (0.67), residues: 58 sheet: -1.62 (0.56), residues: 85 loop : -1.07 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 56 TYR 0.015 0.001 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 0.00371 / 0.21 (10501) covalent geometry : angle 0.51508 / 0.31 (15848) hydrogen bonds : bond 0.06182 / 4.15 ( 392) hydrogen bonds : angle 3.51288 / 2.62 ( 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 28 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 284 GLU cc_start: 0.8159 (mp0) cc_final: 0.7789 (mp0) REVERT: A 375 LEU cc_start: 0.5952 (OUTLIER) cc_final: 0.5722 (tt) REVERT: A 396 ARG cc_start: 0.8229 (ptt-90) cc_final: 0.8021 (ptt-90) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 1.0326 time to fit residues: 25.8797 Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 375 LEU 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: 0.9980 chunk 36 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.109369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071862 restraints weight = 21673.570| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.20 r_work: 0.2947 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10501 Z= 0.125 Angle : 0.459 4.698 15848 Z= 0.286 Chirality : 0.033 0.180 2018 Planarity : 0.004 0.038 725 Dihedral : 21.302 94.869 5348 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.69 % Allowed : 15.61 % 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: -0.76 (0.55), residues: 256 helix: 2.21 (0.67), residues: 58 sheet: -1.59 (0.57), residues: 85 loop : -0.97 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 335 TYR 0.016 0.001 TYR A 405 PHE 0.009 0.001 PHE A 380 TRP 0.005 0.001 TRP A 399 HIS 0.002 0.000 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.12 (10501) covalent geometry : angle 0.45922 / 0.29 (15848) hydrogen bonds : bond 0.05845 / 3.96 ( 392) hydrogen bonds : angle 3.46251 / 2.60 ( 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 26 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8408 (mtp85) cc_final: 0.8016 (mmm-85) REVERT: A 280 GLU cc_start: 0.7605 (tm-30) cc_final: 0.6983 (tm-30) REVERT: A 284 GLU cc_start: 0.8190 (mp0) cc_final: 0.7747 (mp0) REVERT: A 396 ARG cc_start: 0.8220 (ptt-90) cc_final: 0.7922 (ptt-90) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 1.1086 time to fit residues: 26.5800 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 : 0.170 ------------------------------------------------------------------------------- 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: 9.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.103924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.063700 restraints weight = 20252.918| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.39 r_work: 0.2854 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10501 Z= 0.425 Angle : 0.715 9.114 15848 Z= 0.376 Chirality : 0.053 0.239 2018 Planarity : 0.006 0.039 725 Dihedral : 21.292 93.355 5348 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.69 % Allowed : 16.46 % Favored : 81.86 % 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: -1.04 (0.54), residues: 256 helix: 1.89 (0.66), residues: 58 sheet: -1.65 (0.57), residues: 85 loop : -1.19 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 144 TYR 0.015 0.002 TYR A 405 PHE 0.020 0.003 PHE A 380 TRP 0.009 0.003 TRP A 152 HIS 0.005 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.42 (10501) covalent geometry : angle 0.71507 / 0.38 (15848) hydrogen bonds : bond 0.07296 / 4.86 ( 392) hydrogen bonds : angle 3.69467 / 2.77 ( 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 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 284 GLU cc_start: 0.8182 (mp0) cc_final: 0.7647 (mp0) REVERT: A 396 ARG cc_start: 0.8217 (ptt-90) cc_final: 0.8001 (ptt-90) outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 1.0232 time to fit residues: 23.4911 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 : 0.192 ------------------------------------------------------------------------------- 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: 0.7980 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.106946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.067220 restraints weight = 20514.069| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.25 r_work: 0.2950 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10501 Z= 0.133 Angle : 0.483 8.967 15848 Z= 0.291 Chirality : 0.033 0.173 2018 Planarity : 0.005 0.048 725 Dihedral : 21.311 95.476 5348 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.84 % Allowed : 17.30 % Favored : 81.86 % 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: -0.79 (0.55), residues: 256 helix: 2.26 (0.67), residues: 58 sheet: -1.66 (0.57), residues: 85 loop : -0.99 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 56 TYR 0.014 0.001 TYR A 405 PHE 0.007 0.001 PHE A 380 TRP 0.006 0.001 TRP A 399 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (10501) covalent geometry : angle 0.48323 / 0.29 (15848) hydrogen bonds : bond 0.05723 / 3.88 ( 392) hydrogen bonds : angle 3.37812 / 2.54 ( 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 24 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8145 (mtp85) REVERT: A 280 GLU cc_start: 0.7618 (tm-30) cc_final: 0.6997 (tm-30) REVERT: A 284 GLU cc_start: 0.8280 (mp0) cc_final: 0.7845 (mp0) REVERT: A 396 ARG cc_start: 0.8207 (ptt-90) cc_final: 0.7962 (ptt-90) outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 1.0369 time to fit residues: 24.8732 Evaluate side-chains 23 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG 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: 0.7980 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 40.0000 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.103499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.061423 restraints weight = 19611.847| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.27 r_work: 0.2880 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10501 Z= 0.183 Angle : 0.490 8.910 15848 Z= 0.292 Chirality : 0.035 0.170 2018 Planarity : 0.005 0.044 725 Dihedral : 21.261 95.470 5348 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.84 % Allowed : 17.30 % Favored : 81.86 % 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: -0.70 (0.55), residues: 256 helix: 2.34 (0.67), residues: 58 sheet: -1.63 (0.57), residues: 85 loop : -0.91 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 56 TYR 0.015 0.001 TYR A 405 PHE 0.010 0.002 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 0.00317 / 0.18 (10501) covalent geometry : angle 0.49026 / 0.29 (15848) hydrogen bonds : bond 0.05765 / 3.87 ( 392) hydrogen bonds : angle 3.39391 / 2.54 ( 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: 2 poor density : 23 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8194 (mtp85) REVERT: A 280 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6816 (tm-30) REVERT: A 284 GLU cc_start: 0.8159 (mp0) cc_final: 0.7704 (mp0) REVERT: A 396 ARG cc_start: 0.8142 (ptt-90) cc_final: 0.7861 (ptt-90) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 1.0619 time to fit residues: 26.6832 Evaluate side-chains 23 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.105156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065109 restraints weight = 20661.322| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.27 r_work: 0.2848 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2661 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= 0.262 Angle : 0.557 8.706 15848 Z= 0.317 Chirality : 0.041 0.170 2018 Planarity : 0.005 0.042 725 Dihedral : 21.252 95.020 5348 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.42 % Allowed : 17.30 % Favored : 82.28 % 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: -0.77 (0.55), residues: 256 helix: 2.29 (0.68), residues: 58 sheet: -1.62 (0.57), residues: 85 loop : -1.00 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 56 TYR 0.016 0.002 TYR A 405 PHE 0.014 0.002 PHE A 380 TRP 0.006 0.002 TRP A 399 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.26 (10501) covalent geometry : angle 0.55729 / 0.32 (15848) hydrogen bonds : bond 0.06170 / 4.12 ( 392) hydrogen bonds : angle 3.47533 / 2.60 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3245.91 seconds wall clock time: 56 minutes 2.31 seconds (3362.31 seconds total)