Starting phenix.real_space_refine on Tue Feb 3 12:57:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jby_61330/02_2026/9jby_61330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jby_61330/02_2026/9jby_61330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jby_61330/02_2026/9jby_61330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jby_61330/02_2026/9jby_61330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jby_61330/02_2026/9jby_61330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jby_61330/02_2026/9jby_61330.map" } resolution = 3.49 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= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 1662 2.51 5 N 444 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2640 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 440 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.30, per 1000 atoms: 0.11 Number of scatterers: 2640 At special positions: 0 Unit cell: (98.77, 82.17, 32.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 534 8.00 N 444 7.00 C 1662 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: 0.13 Conformation dependent library (CDL) restraints added in 70.8 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 48 through 55 removed outlier: 6.739A pdb=" N VAL A 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N HIS C 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP A 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N VAL A 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N ASP E 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS A 50 " --> pdb=" O ASP E 51 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR E 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A 52 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL E 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR A 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 61 removed outlier: 5.857A pdb=" N THR A 59 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 74 through 79 removed outlier: 6.428A pdb=" N VAL A 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL E 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.512A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 48 through 55 removed outlier: 6.739A pdb=" N VAL B 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS D 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP B 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ASP F 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS B 50 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR F 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 52 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL F 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR B 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 59 through 61 removed outlier: 5.862A pdb=" N THR B 59 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 74 through 78 removed outlier: 6.429A pdb=" N VAL B 74 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL F 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA B 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AA9, first strand: chain 'D' and resid 88 through 89 removed outlier: 6.518A pdb=" N ILE B 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.29 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 462 1.28 - 1.35: 402 1.35 - 1.41: 156 1.41 - 1.48: 444 1.48 - 1.54: 1200 Bond restraints: 2664 Sorted by residual: bond pdb=" CA GLN F 79 " pdb=" CB GLN F 79 " ideal model delta sigma weight residual 1.535 1.507 0.028 1.93e-02 2.68e+03 2.04e+00 bond pdb=" CA GLN B 79 " pdb=" CB GLN B 79 " ideal model delta sigma weight residual 1.535 1.508 0.027 1.93e-02 2.68e+03 1.94e+00 bond pdb=" CA GLN D 79 " pdb=" CB GLN D 79 " ideal model delta sigma weight residual 1.535 1.508 0.027 1.93e-02 2.68e+03 1.94e+00 bond pdb=" CA GLN E 79 " pdb=" CB GLN E 79 " ideal model delta sigma weight residual 1.535 1.509 0.026 1.93e-02 2.68e+03 1.85e+00 bond pdb=" CA GLN A 79 " pdb=" CB GLN A 79 " ideal model delta sigma weight residual 1.535 1.509 0.026 1.93e-02 2.68e+03 1.77e+00 ... (remaining 2659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 3197 1.18 - 2.35: 377 2.35 - 3.53: 32 3.53 - 4.71: 6 4.71 - 5.89: 12 Bond angle restraints: 3624 Sorted by residual: angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 121.75 116.83 4.92 1.73e+00 3.34e-01 8.09e+00 angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 121.75 116.84 4.91 1.73e+00 3.34e-01 8.05e+00 angle pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta sigma weight residual 121.75 116.84 4.91 1.73e+00 3.34e-01 8.04e+00 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 121.75 116.85 4.90 1.73e+00 3.34e-01 8.04e+00 angle pdb=" C VAL F 49 " pdb=" N HIS F 50 " pdb=" CA HIS F 50 " ideal model delta sigma weight residual 121.75 116.85 4.90 1.73e+00 3.34e-01 8.01e+00 ... (remaining 3619 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 9.88: 1192 9.88 - 19.75: 266 19.75 - 29.63: 48 29.63 - 39.50: 18 39.50 - 49.37: 6 Dihedral angle restraints: 1530 sinusoidal: 510 harmonic: 1020 Sorted by residual: dihedral pdb=" CA TYR F 39 " pdb=" C TYR F 39 " pdb=" N VAL F 40 " pdb=" CA VAL F 40 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA TYR B 39 " pdb=" C TYR B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA TYR E 39 " pdb=" C TYR E 39 " pdb=" N VAL E 40 " pdb=" CA VAL E 40 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 1527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 215 0.033 - 0.066: 120 0.066 - 0.098: 70 0.098 - 0.131: 45 0.131 - 0.164: 24 Chirality restraints: 474 Sorted by residual: chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 471 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 50 " -0.010 2.00e-02 2.50e+03 8.99e-03 1.21e+00 pdb=" CG HIS D 50 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS D 50 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS D 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS D 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS D 50 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " -0.010 2.00e-02 2.50e+03 8.88e-03 1.18e+00 pdb=" CG HIS B 50 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " -0.009 2.00e-02 2.50e+03 8.83e-03 1.17e+00 pdb=" CG HIS E 50 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " -0.002 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 951 2.84 - 3.35: 2300 3.35 - 3.87: 4073 3.87 - 4.38: 3893 4.38 - 4.90: 8853 Nonbonded interactions: 20070 Sorted by model distance: nonbonded pdb=" ND2 ASN B 65 " pdb=" O GLY B 68 " model vdw 2.324 3.120 nonbonded pdb=" ND2 ASN F 65 " pdb=" O GLY F 68 " model vdw 2.324 3.120 nonbonded pdb=" ND2 ASN C 65 " pdb=" O GLY C 68 " model vdw 2.324 3.120 nonbonded pdb=" ND2 ASN A 65 " pdb=" O GLY A 68 " model vdw 2.324 3.120 nonbonded pdb=" ND2 ASN D 65 " pdb=" O GLY D 68 " model vdw 2.324 3.120 ... (remaining 20065 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.850 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.640 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.008 0.040 2664 Z= 0.368 Angle : 0.833 5.886 3624 Z= 0.494 Chirality : 0.064 0.164 474 Planarity : 0.003 0.010 444 Dihedral : 12.323 49.371 882 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.89 (0.24), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.19), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.004 TYR C 39 PHE 0.004 0.001 PHE F 94 TRP 0.006 0.002 TRP E 58 HIS 0.009 0.005 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00803 ( 2664) covalent geometry : angle 0.83349 ( 3624) hydrogen bonds : bond 0.20852 ( 24) hydrogen bonds : angle 10.15713 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8650 (m-30) cc_final: 0.8372 (m-30) REVERT: A 58 TRP cc_start: 0.8660 (m100) cc_final: 0.7726 (m100) REVERT: B 51 ASP cc_start: 0.8650 (m-30) cc_final: 0.8408 (m-30) REVERT: B 58 TRP cc_start: 0.8633 (m100) cc_final: 0.7593 (m100) REVERT: C 58 TRP cc_start: 0.8391 (m100) cc_final: 0.7749 (m100) REVERT: E 58 TRP cc_start: 0.8271 (m100) cc_final: 0.7711 (m100) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0464 time to fit residues: 2.1236 Evaluate side-chains 34 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.187610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.165957 restraints weight = 2811.321| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.46 r_work: 0.4256 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4136 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2664 Z= 0.123 Angle : 0.590 4.958 3624 Z= 0.327 Chirality : 0.055 0.157 474 Planarity : 0.002 0.008 444 Dihedral : 6.037 15.056 372 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.36 % Allowed : 10.14 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR D 39 PHE 0.006 0.001 PHE B 94 TRP 0.004 0.001 TRP B 58 HIS 0.004 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2664) covalent geometry : angle 0.58958 ( 3624) hydrogen bonds : bond 0.02414 ( 24) hydrogen bonds : angle 5.18161 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 TRP cc_start: 0.8759 (m100) cc_final: 0.8077 (m100) REVERT: C 58 TRP cc_start: 0.8481 (m100) cc_final: 0.8189 (m100) REVERT: C 62 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7822 (tm-30) REVERT: D 58 TRP cc_start: 0.8344 (m100) cc_final: 0.7654 (m100) REVERT: D 62 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8256 (tm-30) REVERT: F 58 TRP cc_start: 0.8401 (m100) cc_final: 0.7912 (m100) outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.0761 time to fit residues: 3.2650 Evaluate side-chains 28 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.174102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.150403 restraints weight = 2958.680| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.89 r_work: 0.4163 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2664 Z= 0.209 Angle : 0.652 5.497 3624 Z= 0.364 Chirality : 0.058 0.162 474 Planarity : 0.002 0.007 444 Dihedral : 6.305 15.179 372 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 2.17 % Allowed : 11.23 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.31), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.24), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.003 TYR D 39 PHE 0.005 0.001 PHE B 94 TRP 0.005 0.002 TRP D 58 HIS 0.006 0.003 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 2664) covalent geometry : angle 0.65229 ( 3624) hydrogen bonds : bond 0.02263 ( 24) hydrogen bonds : angle 4.83880 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 TRP cc_start: 0.8702 (m100) cc_final: 0.7885 (m100) REVERT: A 97 LYS cc_start: 0.8426 (mtmt) cc_final: 0.7851 (mtmm) REVERT: B 58 TRP cc_start: 0.8684 (m100) cc_final: 0.7744 (m100) REVERT: C 58 TRP cc_start: 0.8457 (m100) cc_final: 0.8041 (m100) REVERT: C 62 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7935 (tm-30) outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.0469 time to fit residues: 1.9760 Evaluate side-chains 31 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.187736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.165719 restraints weight = 2831.926| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.51 r_work: 0.4219 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2664 Z= 0.147 Angle : 0.570 4.531 3624 Z= 0.319 Chirality : 0.055 0.152 474 Planarity : 0.002 0.006 444 Dihedral : 5.849 14.497 372 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.17 % Allowed : 11.59 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.32), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.24), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR D 39 PHE 0.004 0.001 PHE A 94 TRP 0.003 0.001 TRP C 58 HIS 0.005 0.003 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2664) covalent geometry : angle 0.57046 ( 3624) hydrogen bonds : bond 0.01662 ( 24) hydrogen bonds : angle 4.19075 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 TRP cc_start: 0.8682 (m100) cc_final: 0.7958 (m100) REVERT: C 58 TRP cc_start: 0.8442 (m100) cc_final: 0.8094 (m100) REVERT: C 62 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 58 TRP cc_start: 0.8287 (m100) cc_final: 0.7607 (m100) REVERT: F 58 TRP cc_start: 0.8203 (m100) cc_final: 0.7743 (m100) outliers start: 6 outliers final: 3 residues processed: 34 average time/residue: 0.0476 time to fit residues: 1.9608 Evaluate side-chains 28 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.180430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.157184 restraints weight = 3012.154| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.98 r_work: 0.4195 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2664 Z= 0.135 Angle : 0.550 6.244 3624 Z= 0.303 Chirality : 0.054 0.149 474 Planarity : 0.002 0.005 444 Dihedral : 5.530 13.988 372 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.90 % Allowed : 12.68 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.32), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR E 39 PHE 0.005 0.001 PHE B 94 TRP 0.003 0.001 TRP C 58 HIS 0.005 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2664) covalent geometry : angle 0.54954 ( 3624) hydrogen bonds : bond 0.01438 ( 24) hydrogen bonds : angle 3.92367 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 TRP cc_start: 0.8672 (m100) cc_final: 0.7902 (m100) REVERT: B 97 LYS cc_start: 0.8353 (mtmt) cc_final: 0.7839 (mtmm) REVERT: C 58 TRP cc_start: 0.8457 (m100) cc_final: 0.8071 (m100) REVERT: D 58 TRP cc_start: 0.8281 (m100) cc_final: 0.7622 (m100) REVERT: F 58 TRP cc_start: 0.8124 (m100) cc_final: 0.7617 (m100) outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.0506 time to fit residues: 1.8711 Evaluate side-chains 26 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.0020 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.186756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.164175 restraints weight = 2806.223| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.58 r_work: 0.4262 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2664 Z= 0.145 Angle : 0.564 6.054 3624 Z= 0.309 Chirality : 0.054 0.151 474 Planarity : 0.002 0.006 444 Dihedral : 5.520 14.223 372 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.26 % Allowed : 12.32 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR B 39 PHE 0.004 0.001 PHE B 94 TRP 0.003 0.001 TRP D 58 HIS 0.005 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2664) covalent geometry : angle 0.56407 ( 3624) hydrogen bonds : bond 0.01381 ( 24) hydrogen bonds : angle 3.89990 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 58 TRP cc_start: 0.8742 (m100) cc_final: 0.8032 (m100) REVERT: B 58 TRP cc_start: 0.8706 (m100) cc_final: 0.7770 (m100) REVERT: C 58 TRP cc_start: 0.8469 (m100) cc_final: 0.8107 (m100) outliers start: 9 outliers final: 6 residues processed: 29 average time/residue: 0.0606 time to fit residues: 2.1377 Evaluate side-chains 25 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.184462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.161973 restraints weight = 2845.980| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.56 r_work: 0.4233 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4112 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2664 Z= 0.182 Angle : 0.604 6.094 3624 Z= 0.333 Chirality : 0.055 0.155 474 Planarity : 0.002 0.007 444 Dihedral : 5.783 14.870 372 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.26 % Allowed : 13.04 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR B 39 PHE 0.004 0.001 PHE A 94 TRP 0.004 0.001 TRP E 58 HIS 0.006 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 2664) covalent geometry : angle 0.60357 ( 3624) hydrogen bonds : bond 0.01460 ( 24) hydrogen bonds : angle 4.10946 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 TRP cc_start: 0.8740 (m100) cc_final: 0.7981 (m100) REVERT: B 58 TRP cc_start: 0.8702 (m100) cc_final: 0.7748 (m100) REVERT: C 58 TRP cc_start: 0.8493 (m100) cc_final: 0.8072 (m100) outliers start: 9 outliers final: 7 residues processed: 29 average time/residue: 0.0823 time to fit residues: 2.8770 Evaluate side-chains 27 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.0060 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.190435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.169035 restraints weight = 2816.573| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 2.40 r_work: 0.4305 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4187 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2664 Z= 0.116 Angle : 0.533 5.314 3624 Z= 0.293 Chirality : 0.053 0.145 474 Planarity : 0.001 0.005 444 Dihedral : 5.251 13.808 372 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.81 % Allowed : 14.49 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR B 39 PHE 0.004 0.001 PHE A 94 TRP 0.003 0.001 TRP E 58 HIS 0.005 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 2664) covalent geometry : angle 0.53337 ( 3624) hydrogen bonds : bond 0.01117 ( 24) hydrogen bonds : angle 3.70008 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 TRP cc_start: 0.8669 (m100) cc_final: 0.7789 (m100) REVERT: C 58 TRP cc_start: 0.8435 (m100) cc_final: 0.8089 (m100) REVERT: E 58 TRP cc_start: 0.7876 (m100) cc_final: 0.7345 (m100) outliers start: 5 outliers final: 1 residues processed: 26 average time/residue: 0.0858 time to fit residues: 2.6480 Evaluate side-chains 20 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 0.0770 chunk 11 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.190716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.168814 restraints weight = 2809.144| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.47 r_work: 0.4293 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4174 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2664 Z= 0.117 Angle : 0.543 9.066 3624 Z= 0.289 Chirality : 0.052 0.145 474 Planarity : 0.002 0.006 444 Dihedral : 5.090 13.219 372 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.45 % Allowed : 14.13 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR B 39 PHE 0.004 0.001 PHE A 94 TRP 0.004 0.001 TRP E 58 HIS 0.006 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 2664) covalent geometry : angle 0.54342 ( 3624) hydrogen bonds : bond 0.01006 ( 24) hydrogen bonds : angle 3.65291 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 TRP cc_start: 0.8681 (m100) cc_final: 0.7785 (m100) REVERT: C 58 TRP cc_start: 0.8422 (m100) cc_final: 0.8062 (m100) REVERT: E 58 TRP cc_start: 0.7876 (m100) cc_final: 0.7312 (m100) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.0950 time to fit residues: 2.7079 Evaluate side-chains 22 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.172859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.149691 restraints weight = 3040.551| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.84 r_work: 0.4113 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 2664 Z= 0.333 Angle : 0.759 9.070 3624 Z= 0.421 Chirality : 0.061 0.172 474 Planarity : 0.003 0.011 444 Dihedral : 6.792 16.053 372 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 1.45 % Allowed : 14.13 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.003 TYR B 39 PHE 0.005 0.002 PHE B 94 TRP 0.014 0.003 TRP F 58 HIS 0.009 0.005 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00732 ( 2664) covalent geometry : angle 0.75896 ( 3624) hydrogen bonds : bond 0.02013 ( 24) hydrogen bonds : angle 4.83887 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 TRP cc_start: 0.8705 (m100) cc_final: 0.7986 (m100) REVERT: B 58 TRP cc_start: 0.8666 (m100) cc_final: 0.7729 (m100) REVERT: C 58 TRP cc_start: 0.8474 (m100) cc_final: 0.7980 (m100) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.0759 time to fit residues: 2.9818 Evaluate side-chains 32 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.186251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.165236 restraints weight = 2856.277| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.51 r_work: 0.4243 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2664 Z= 0.120 Angle : 0.575 8.141 3624 Z= 0.310 Chirality : 0.054 0.148 474 Planarity : 0.002 0.006 444 Dihedral : 5.464 13.569 372 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.45 % Allowed : 14.86 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR E 39 PHE 0.004 0.001 PHE B 94 TRP 0.006 0.001 TRP E 58 HIS 0.006 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2664) covalent geometry : angle 0.57499 ( 3624) hydrogen bonds : bond 0.01053 ( 24) hydrogen bonds : angle 3.80781 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 755.95 seconds wall clock time: 13 minutes 43.04 seconds (823.04 seconds total)