Starting phenix.real_space_refine on Wed May 14 22:53:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl0_16708/05_2025/8cl0_16708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl0_16708/05_2025/8cl0_16708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cl0_16708/05_2025/8cl0_16708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl0_16708/05_2025/8cl0_16708.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl0_16708/05_2025/8cl0_16708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl0_16708/05_2025/8cl0_16708.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2586 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6567 2.51 5 N 1799 2.21 5 O 1949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10387 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1644 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1650 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "C" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1652 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "D" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1645 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "F" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1651 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Time building chain proxies: 6.41, per 1000 atoms: 0.62 Number of scatterers: 10387 At special positions: 0 Unit cell: (113.46, 109.74, 75.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1949 8.00 N 1799 7.00 C 6567 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 6 sheets defined 69.2% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.634A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.396A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.650A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.666A pdb=" N VAL B 59 " --> pdb=" O MET B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.669A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.517A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 removed outlier: 4.224A pdb=" N THR B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 45 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.627A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.633A pdb=" N LYS C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.145A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.762A pdb=" N THR C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.586A pdb=" N VAL D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.167A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.997A pdb=" N THR D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.657A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.540A pdb=" N LYS E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.452A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.760A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 59 removed outlier: 3.600A pdb=" N VAL F 59 " --> pdb=" O MET F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 146 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.001A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 removed outlier: 3.716A pdb=" N THR F 200 " --> pdb=" O PRO F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 4 639 hydrogen bonds defined for protein. 1887 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: 2.62 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3380 1.34 - 1.46: 1099 1.46 - 1.57: 5998 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 10609 Sorted by residual: bond pdb=" CB GLU D 35 " pdb=" CG GLU D 35 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.27e+00 bond pdb=" N ASN L1409 " pdb=" CA ASN L1409 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.90e-02 2.77e+03 5.74e+00 bond pdb=" N ASN J1409 " pdb=" CA ASN J1409 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.63e+00 bond pdb=" CA ASN J1409 " pdb=" C ASN J1409 " ideal model delta sigma weight residual 1.525 1.569 -0.044 2.10e-02 2.27e+03 4.47e+00 bond pdb=" N ASN H1409 " pdb=" CA ASN H1409 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.26e+00 ... (remaining 10604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 13515 1.63 - 3.27: 801 3.27 - 4.90: 84 4.90 - 6.53: 18 6.53 - 8.17: 3 Bond angle restraints: 14421 Sorted by residual: angle pdb=" CA VAL F 3 " pdb=" CB VAL F 3 " pdb=" CG1 VAL F 3 " ideal model delta sigma weight residual 110.40 118.57 -8.17 1.70e+00 3.46e-01 2.31e+01 angle pdb=" CA VAL F 3 " pdb=" CB VAL F 3 " pdb=" CG2 VAL F 3 " ideal model delta sigma weight residual 110.40 116.14 -5.74 1.70e+00 3.46e-01 1.14e+01 angle pdb=" CA GLU D 45 " pdb=" CB GLU D 45 " pdb=" CG GLU D 45 " ideal model delta sigma weight residual 114.10 107.40 6.70 2.00e+00 2.50e-01 1.12e+01 angle pdb=" N SER C 44 " pdb=" CA SER C 44 " pdb=" C SER C 44 " ideal model delta sigma weight residual 111.71 115.55 -3.84 1.15e+00 7.56e-01 1.12e+01 angle pdb=" CG1 VAL F 3 " pdb=" CB VAL F 3 " pdb=" CG2 VAL F 3 " ideal model delta sigma weight residual 110.80 117.88 -7.08 2.20e+00 2.07e-01 1.04e+01 ... (remaining 14416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6032 17.88 - 35.75: 319 35.75 - 53.63: 63 53.63 - 71.51: 16 71.51 - 89.39: 13 Dihedral angle restraints: 6443 sinusoidal: 2552 harmonic: 3891 Sorted by residual: dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N SER E 33 " pdb=" CA SER E 33 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA PHE C 32 " pdb=" C PHE C 32 " pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PHE B 32 " pdb=" C PHE B 32 " pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 6440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 1634 0.222 - 0.444: 4 0.444 - 0.667: 0 0.667 - 0.889: 0 0.889 - 1.111: 1 Chirality restraints: 1639 Sorted by residual: chirality pdb=" CB VAL F 3 " pdb=" CA VAL F 3 " pdb=" CG1 VAL F 3 " pdb=" CG2 VAL F 3 " both_signs ideal model delta sigma weight residual False -2.63 -1.52 -1.11 2.00e-01 2.50e+01 3.09e+01 chirality pdb=" CA ASN H1409 " pdb=" N ASN H1409 " pdb=" C ASN H1409 " pdb=" CB ASN H1409 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASN K1409 " pdb=" N ASN K1409 " pdb=" C ASN K1409 " pdb=" CB ASN K1409 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1636 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 97 " 0.318 9.50e-02 1.11e+02 1.43e-01 1.32e+01 pdb=" NE ARG C 97 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 97 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 97 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 97 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 97 " 0.303 9.50e-02 1.11e+02 1.36e-01 1.24e+01 pdb=" NE ARG B 97 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 97 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 97 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 97 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 52 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C LEU A 52 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 52 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 53 " 0.018 2.00e-02 2.50e+03 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 66 2.65 - 3.21: 10322 3.21 - 3.78: 16474 3.78 - 4.34: 23328 4.34 - 4.90: 37545 Nonbonded interactions: 87735 Sorted by model distance: nonbonded pdb=" OG1 THR E 110 " pdb=" OE1 GLU E 113 " model vdw 2.091 3.040 nonbonded pdb=" NH1 ARG E 143 " pdb=" O ASN L1409 " model vdw 2.372 3.120 nonbonded pdb=" OG SER D 33 " pdb=" OE1 GLU D 35 " model vdw 2.437 3.040 nonbonded pdb=" OG SER C 33 " pdb=" OE1 GLU C 35 " model vdw 2.480 3.040 nonbonded pdb=" O THR A 54 " pdb=" OG1 THR A 58 " model vdw 2.481 3.040 ... (remaining 87730 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 87 or resid 96 through 151 or (resid 152 and (na \ me N or name CA or name C or name O or name CB )) or resid 153 through 157 or (r \ esid 158 and (name N or name CA or name C or name O or name CB )) or resid 159 t \ hrough 221)) selection = (chain 'B' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 or (resid 9 through 10 and (name N o \ r name CA or name C or name O or name CB )) or resid 11 through 12 or (resid 13 \ through 14 and (name N or name CA or name C or name O or name CB )) or resid 15 \ through 151 or (resid 152 and (name N or name CA or name C or name O or name CB \ )) or resid 153 through 221)) selection = (chain 'C' and (resid 1 through 4 or (resid 5 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 12 or (resid 13 through 14 a \ nd (name N or name CA or name C or name O or name CB )) or resid 15 through 87 o \ r resid 96 through 151 or (resid 152 and (name N or name CA or name C or name O \ or name CB )) or resid 153 through 221)) selection = (chain 'D' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 12 or (resid 13 through 14 a \ nd (name N or name CA or name C or name O or name CB )) or resid 15 through 87 o \ r resid 96 through 221)) selection = (chain 'E' and (resid 1 through 8 or (resid 9 through 10 and (name N or name CA \ or name C or name O or name CB )) or resid 11 through 12 or (resid 13 through 14 \ and (name N or name CA or name C or name O or name CB )) or resid 15 through 87 \ or resid 96 through 157 or (resid 158 and (name N or name CA or name C or name \ O or name CB )) or resid 159 through 221)) selection = (chain 'F' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 12 or (resid 13 through 14 a \ nd (name N or name CA or name C or name O or name CB )) or resid 15 through 87 o \ r resid 96 through 151 or (resid 152 and (name N or name CA or name C or name O \ or name CB )) or resid 153 through 221)) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 1410 through 1420) selection = (chain 'I' and resid 1410 through 1420) selection = (chain 'J' and resid 1410 through 1420) selection = (chain 'K' and resid 1410 through 1420) selection = (chain 'L' and resid 1410 through 1420) } 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.960 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.005 0.079 10609 Z= 0.264 Angle : 0.869 8.165 14421 Z= 0.525 Chirality : 0.059 1.111 1639 Planarity : 0.011 0.143 1867 Dihedral : 12.800 89.386 3913 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.18 % Allowed : 0.09 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1319 helix: -0.41 (0.15), residues: 881 sheet: -2.77 (0.43), residues: 45 loop : 0.72 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 117 HIS 0.014 0.003 HIS A 12 PHE 0.012 0.003 PHE H1417 TYR 0.027 0.006 TYR C 169 ARG 0.027 0.003 ARG B 154 Details of bonding type rmsd hydrogen bonds : bond 0.10258 ( 639) hydrogen bonds : angle 5.95054 ( 1887) covalent geometry : bond 0.00543 (10609) covalent geometry : angle 0.86933 (14421) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 1.039 Fit side-chains REVERT: B 76 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7638 (mm-30) REVERT: C 75 GLU cc_start: 0.7167 (tt0) cc_final: 0.6921 (tt0) REVERT: C 140 LYS cc_start: 0.8356 (mttt) cc_final: 0.8072 (mttp) REVERT: D 39 MET cc_start: 0.7727 (tpt) cc_final: 0.7526 (tpt) REVERT: D 219 GLN cc_start: 0.7029 (tt0) cc_final: 0.6815 (tt0) REVERT: E 68 MET cc_start: 0.8257 (mtm) cc_final: 0.7981 (mtt) REVERT: F 108 THR cc_start: 0.8562 (p) cc_final: 0.8273 (p) outliers start: 2 outliers final: 2 residues processed: 224 average time/residue: 0.2223 time to fit residues: 69.1638 Evaluate side-chains 172 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain E residue 96 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.169868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141111 restraints weight = 10991.974| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.04 r_work: 0.3440 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10609 Z= 0.200 Angle : 0.579 6.340 14421 Z= 0.300 Chirality : 0.044 0.169 1639 Planarity : 0.005 0.035 1867 Dihedral : 5.131 54.133 1427 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.45 % Allowed : 3.99 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.22), residues: 1319 helix: 1.03 (0.17), residues: 878 sheet: -2.04 (0.54), residues: 45 loop : 1.03 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 117 HIS 0.003 0.001 HIS D 84 PHE 0.014 0.002 PHE E 32 TYR 0.020 0.002 TYR F 169 ARG 0.004 0.001 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 639) hydrogen bonds : angle 4.27598 ( 1887) covalent geometry : bond 0.00505 (10609) covalent geometry : angle 0.57868 (14421) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 1.176 Fit side-chains REVERT: B 159 GLU cc_start: 0.7994 (tt0) cc_final: 0.7747 (tt0) REVERT: B 187 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: C 29 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7734 (mm-30) REVERT: C 75 GLU cc_start: 0.7881 (tt0) cc_final: 0.7532 (tt0) REVERT: C 140 LYS cc_start: 0.8722 (mttt) cc_final: 0.8352 (mttp) REVERT: C 179 GLN cc_start: 0.8423 (tp40) cc_final: 0.8103 (tp-100) REVERT: C 199 LYS cc_start: 0.7851 (tttm) cc_final: 0.7635 (mtpp) REVERT: D 39 MET cc_start: 0.8406 (tpt) cc_final: 0.8134 (tpt) REVERT: E 103 ASP cc_start: 0.8099 (m-30) cc_final: 0.7799 (m-30) REVERT: E 113 GLU cc_start: 0.8266 (mp0) cc_final: 0.7476 (mp0) REVERT: F 143 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7749 (ttp-170) outliers start: 16 outliers final: 9 residues processed: 188 average time/residue: 0.2435 time to fit residues: 63.3713 Evaluate side-chains 179 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain F residue 35 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.170760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141606 restraints weight = 10953.281| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.10 r_work: 0.3431 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10609 Z= 0.151 Angle : 0.508 5.639 14421 Z= 0.260 Chirality : 0.041 0.152 1639 Planarity : 0.004 0.032 1867 Dihedral : 4.382 46.472 1424 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.72 % Allowed : 4.71 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.22), residues: 1319 helix: 1.44 (0.17), residues: 882 sheet: -0.96 (1.76), residues: 9 loop : 0.92 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 184 HIS 0.002 0.001 HIS D 84 PHE 0.015 0.002 PHE E 32 TYR 0.016 0.001 TYR F 169 ARG 0.002 0.000 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 639) hydrogen bonds : angle 3.89826 ( 1887) covalent geometry : bond 0.00376 (10609) covalent geometry : angle 0.50844 (14421) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.016 Fit side-chains REVERT: A 175 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7318 (mt-10) REVERT: B 159 GLU cc_start: 0.7976 (tt0) cc_final: 0.7735 (tt0) REVERT: B 187 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: C 29 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7727 (mm-30) REVERT: C 140 LYS cc_start: 0.8694 (mttt) cc_final: 0.8428 (mtpp) REVERT: D 39 MET cc_start: 0.8395 (tpt) cc_final: 0.8090 (tpt) REVERT: E 68 MET cc_start: 0.8607 (mtm) cc_final: 0.8360 (mtt) REVERT: E 103 ASP cc_start: 0.8082 (m-30) cc_final: 0.7762 (m-30) REVERT: E 113 GLU cc_start: 0.8247 (mp0) cc_final: 0.7527 (mp0) REVERT: E 180 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6346 (mm-30) REVERT: E 215 MET cc_start: 0.8037 (mtp) cc_final: 0.7454 (mtp) REVERT: F 143 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7595 (ttp80) REVERT: F 172 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7960 (tp) outliers start: 19 outliers final: 9 residues processed: 177 average time/residue: 0.2490 time to fit residues: 59.9568 Evaluate side-chains 167 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 192 GLN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.173793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.145066 restraints weight = 10799.876| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.04 r_work: 0.3441 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10609 Z= 0.141 Angle : 0.490 5.336 14421 Z= 0.249 Chirality : 0.041 0.158 1639 Planarity : 0.004 0.036 1867 Dihedral : 3.970 20.249 1421 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.36 % Allowed : 5.71 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.22), residues: 1319 helix: 1.62 (0.17), residues: 882 sheet: -0.93 (1.68), residues: 9 loop : 0.99 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 184 HIS 0.003 0.001 HIS A 120 PHE 0.014 0.002 PHE E 32 TYR 0.015 0.001 TYR F 169 ARG 0.002 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 639) hydrogen bonds : angle 3.78007 ( 1887) covalent geometry : bond 0.00352 (10609) covalent geometry : angle 0.49012 (14421) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.137 Fit side-chains REVERT: A 175 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7350 (mt-10) REVERT: B 159 GLU cc_start: 0.7946 (tt0) cc_final: 0.7721 (tt0) REVERT: B 187 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: C 29 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7749 (mm-30) REVERT: C 66 MET cc_start: 0.8749 (mmm) cc_final: 0.8343 (mmp) REVERT: C 75 GLU cc_start: 0.7963 (tt0) cc_final: 0.7644 (tt0) REVERT: C 140 LYS cc_start: 0.8710 (mttt) cc_final: 0.8395 (mtpp) REVERT: D 39 MET cc_start: 0.8388 (tpt) cc_final: 0.8134 (tpt) REVERT: E 103 ASP cc_start: 0.8169 (m-30) cc_final: 0.7836 (m-30) REVERT: E 113 GLU cc_start: 0.8251 (mp0) cc_final: 0.7657 (mp0) REVERT: E 180 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6479 (mm-30) REVERT: E 215 MET cc_start: 0.8019 (mtp) cc_final: 0.7461 (mtp) REVERT: F 143 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7576 (ttp80) outliers start: 15 outliers final: 9 residues processed: 173 average time/residue: 0.2477 time to fit residues: 58.5551 Evaluate side-chains 165 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 219 GLN D 219 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141769 restraints weight = 10923.701| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.08 r_work: 0.3398 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10609 Z= 0.196 Angle : 0.531 5.805 14421 Z= 0.269 Chirality : 0.043 0.150 1639 Planarity : 0.005 0.036 1867 Dihedral : 4.101 21.206 1421 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.18 % Allowed : 6.79 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.23), residues: 1319 helix: 1.51 (0.18), residues: 882 sheet: -1.47 (0.62), residues: 45 loop : 1.10 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 80 HIS 0.003 0.001 HIS F 120 PHE 0.014 0.002 PHE E 32 TYR 0.016 0.002 TYR F 169 ARG 0.003 0.000 ARG D 97 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 639) hydrogen bonds : angle 3.87001 ( 1887) covalent geometry : bond 0.00502 (10609) covalent geometry : angle 0.53051 (14421) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 1.038 Fit side-chains REVERT: A 167 ARG cc_start: 0.8314 (mtp180) cc_final: 0.8005 (mtp180) REVERT: A 175 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7411 (mt-10) REVERT: B 76 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7877 (mm-30) REVERT: B 159 GLU cc_start: 0.8032 (tt0) cc_final: 0.7826 (tt0) REVERT: B 187 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: C 66 MET cc_start: 0.8717 (mmm) cc_final: 0.8338 (mmp) REVERT: C 75 GLU cc_start: 0.8034 (tt0) cc_final: 0.7706 (tt0) REVERT: C 140 LYS cc_start: 0.8696 (mttt) cc_final: 0.8379 (mtpp) REVERT: D 79 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6976 (mt-10) REVERT: E 103 ASP cc_start: 0.8155 (m-30) cc_final: 0.7826 (m-30) REVERT: E 113 GLU cc_start: 0.8243 (mp0) cc_final: 0.7538 (mp0) REVERT: F 45 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7402 (mm-30) REVERT: F 172 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7972 (tp) REVERT: F 185 MET cc_start: 0.7861 (mtt) cc_final: 0.7659 (mtm) outliers start: 13 outliers final: 9 residues processed: 178 average time/residue: 0.2380 time to fit residues: 57.9202 Evaluate side-chains 173 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 103 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.172871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143895 restraints weight = 10903.082| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.06 r_work: 0.3430 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10609 Z= 0.150 Angle : 0.496 5.597 14421 Z= 0.251 Chirality : 0.041 0.145 1639 Planarity : 0.004 0.037 1867 Dihedral : 3.933 19.721 1421 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.45 % Allowed : 6.97 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.23), residues: 1319 helix: 1.59 (0.18), residues: 882 sheet: -1.38 (0.62), residues: 45 loop : 1.12 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 184 HIS 0.002 0.001 HIS C 62 PHE 0.014 0.001 PHE E 32 TYR 0.014 0.001 TYR F 169 ARG 0.002 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 639) hydrogen bonds : angle 3.77295 ( 1887) covalent geometry : bond 0.00379 (10609) covalent geometry : angle 0.49615 (14421) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.055 Fit side-chains REVERT: A 175 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7384 (mt-10) REVERT: B 76 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7845 (mm-30) REVERT: B 187 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: C 75 GLU cc_start: 0.7975 (tt0) cc_final: 0.7665 (tt0) REVERT: C 140 LYS cc_start: 0.8696 (mttt) cc_final: 0.8349 (mtpp) REVERT: D 39 MET cc_start: 0.8386 (tpt) cc_final: 0.8116 (tpp) REVERT: D 79 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6974 (mt-10) REVERT: E 103 ASP cc_start: 0.8095 (m-30) cc_final: 0.7764 (m-30) REVERT: E 113 GLU cc_start: 0.8217 (mp0) cc_final: 0.7550 (mp0) REVERT: F 45 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7420 (mm-30) REVERT: F 172 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8006 (tp) outliers start: 16 outliers final: 11 residues processed: 173 average time/residue: 0.2385 time to fit residues: 56.4387 Evaluate side-chains 173 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 11 optimal weight: 0.1980 chunk 93 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN F 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.174823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145765 restraints weight = 11004.793| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.09 r_work: 0.3449 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10609 Z= 0.126 Angle : 0.483 7.167 14421 Z= 0.244 Chirality : 0.040 0.141 1639 Planarity : 0.004 0.037 1867 Dihedral : 3.777 19.173 1421 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.36 % Allowed : 7.52 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.23), residues: 1319 helix: 1.71 (0.18), residues: 886 sheet: -1.28 (0.63), residues: 45 loop : 1.17 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 184 HIS 0.002 0.000 HIS D 84 PHE 0.015 0.001 PHE C 32 TYR 0.013 0.001 TYR F 169 ARG 0.005 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 639) hydrogen bonds : angle 3.68092 ( 1887) covalent geometry : bond 0.00314 (10609) covalent geometry : angle 0.48262 (14421) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.493 Fit side-chains REVERT: A 167 ARG cc_start: 0.8275 (mtp180) cc_final: 0.8033 (mtp180) REVERT: A 175 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: A 212 GLU cc_start: 0.7705 (tp30) cc_final: 0.7452 (tp30) REVERT: B 76 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7859 (mm-30) REVERT: B 187 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: C 75 GLU cc_start: 0.7978 (tt0) cc_final: 0.7684 (tt0) REVERT: C 140 LYS cc_start: 0.8681 (mttt) cc_final: 0.8324 (mtpp) REVERT: D 39 MET cc_start: 0.8351 (tpt) cc_final: 0.8127 (tpp) REVERT: E 103 ASP cc_start: 0.8074 (m-30) cc_final: 0.7741 (m-30) REVERT: E 113 GLU cc_start: 0.8165 (mp0) cc_final: 0.7602 (mp0) REVERT: E 215 MET cc_start: 0.7977 (mtp) cc_final: 0.7338 (mtp) REVERT: F 45 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7404 (mm-30) REVERT: F 154 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7581 (mtp180) REVERT: F 172 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7999 (tp) outliers start: 15 outliers final: 10 residues processed: 161 average time/residue: 0.2619 time to fit residues: 57.4330 Evaluate side-chains 166 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.0030 overall best weight: 0.7152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.170516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141138 restraints weight = 10986.145| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.09 r_work: 0.3441 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10609 Z= 0.143 Angle : 0.493 5.812 14421 Z= 0.248 Chirality : 0.041 0.141 1639 Planarity : 0.004 0.037 1867 Dihedral : 3.789 19.608 1421 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.36 % Allowed : 7.52 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.23), residues: 1319 helix: 1.69 (0.18), residues: 886 sheet: -1.41 (0.57), residues: 54 loop : 1.21 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 80 HIS 0.002 0.001 HIS F 12 PHE 0.012 0.001 PHE C 32 TYR 0.013 0.001 TYR F 169 ARG 0.004 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 639) hydrogen bonds : angle 3.70690 ( 1887) covalent geometry : bond 0.00361 (10609) covalent geometry : angle 0.49281 (14421) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: B 76 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7880 (mm-30) REVERT: B 187 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: C 29 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7752 (mm-30) REVERT: C 75 GLU cc_start: 0.7986 (tt0) cc_final: 0.7707 (tt0) REVERT: C 140 LYS cc_start: 0.8675 (mttt) cc_final: 0.8330 (mtpp) REVERT: D 39 MET cc_start: 0.8354 (tpt) cc_final: 0.8110 (tpp) REVERT: E 103 ASP cc_start: 0.8124 (m-30) cc_final: 0.7774 (m-30) REVERT: E 113 GLU cc_start: 0.8227 (mp0) cc_final: 0.7609 (mp0) REVERT: E 215 MET cc_start: 0.8002 (mtp) cc_final: 0.7712 (mtp) REVERT: F 45 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7427 (mm-30) REVERT: F 143 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7663 (ttp80) REVERT: F 172 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7990 (tp) outliers start: 15 outliers final: 11 residues processed: 165 average time/residue: 0.2470 time to fit residues: 55.6842 Evaluate side-chains 168 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 127 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 126 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.171584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142344 restraints weight = 10972.752| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.09 r_work: 0.3454 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10609 Z= 0.128 Angle : 0.486 5.488 14421 Z= 0.246 Chirality : 0.040 0.139 1639 Planarity : 0.004 0.037 1867 Dihedral : 3.722 19.139 1421 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.36 % Allowed : 8.24 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.23), residues: 1319 helix: 1.75 (0.18), residues: 886 sheet: -1.37 (0.58), residues: 54 loop : 1.20 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 184 HIS 0.002 0.000 HIS F 12 PHE 0.012 0.001 PHE C 32 TYR 0.013 0.001 TYR F 169 ARG 0.002 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 639) hydrogen bonds : angle 3.68212 ( 1887) covalent geometry : bond 0.00319 (10609) covalent geometry : angle 0.48599 (14421) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.121 Fit side-chains REVERT: A 175 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: B 76 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 187 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: C 29 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7670 (mm-30) REVERT: C 75 GLU cc_start: 0.7999 (tt0) cc_final: 0.7484 (pt0) REVERT: C 140 LYS cc_start: 0.8673 (mttt) cc_final: 0.8357 (mtpp) REVERT: D 39 MET cc_start: 0.8317 (tpt) cc_final: 0.7723 (tpt) REVERT: E 103 ASP cc_start: 0.8117 (m-30) cc_final: 0.7771 (m-30) REVERT: E 113 GLU cc_start: 0.8219 (mp0) cc_final: 0.7611 (mp0) REVERT: E 180 GLU cc_start: 0.7527 (tm-30) cc_final: 0.6679 (mm-30) REVERT: E 215 MET cc_start: 0.7981 (mtp) cc_final: 0.7655 (mtp) REVERT: F 45 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7375 (mm-30) REVERT: F 154 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7597 (mtp180) REVERT: F 172 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7994 (tp) outliers start: 15 outliers final: 10 residues processed: 163 average time/residue: 0.2575 time to fit residues: 56.8818 Evaluate side-chains 167 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 103 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.174562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145635 restraints weight = 10979.279| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.07 r_work: 0.3453 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10609 Z= 0.131 Angle : 0.492 6.672 14421 Z= 0.249 Chirality : 0.040 0.139 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.719 19.157 1421 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.36 % Allowed : 8.33 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.23), residues: 1319 helix: 1.71 (0.18), residues: 892 sheet: -1.34 (0.58), residues: 54 loop : 1.19 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 80 HIS 0.002 0.000 HIS F 12 PHE 0.012 0.001 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.002 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 639) hydrogen bonds : angle 3.69562 ( 1887) covalent geometry : bond 0.00328 (10609) covalent geometry : angle 0.49220 (14421) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: B 76 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7847 (mm-30) REVERT: B 187 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: C 29 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7642 (mm-30) REVERT: C 75 GLU cc_start: 0.8005 (tt0) cc_final: 0.7493 (pt0) REVERT: C 140 LYS cc_start: 0.8650 (mttt) cc_final: 0.8343 (mtpp) REVERT: D 39 MET cc_start: 0.8323 (tpt) cc_final: 0.7724 (tpt) REVERT: E 103 ASP cc_start: 0.8127 (m-30) cc_final: 0.7778 (m-30) REVERT: E 113 GLU cc_start: 0.8235 (mp0) cc_final: 0.7609 (mp0) REVERT: E 215 MET cc_start: 0.7988 (mtp) cc_final: 0.7668 (mtp) REVERT: F 45 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7383 (mm-30) REVERT: F 143 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7617 (ttp80) REVERT: F 154 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7611 (mtp180) REVERT: F 172 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7999 (tp) outliers start: 15 outliers final: 11 residues processed: 160 average time/residue: 0.2508 time to fit residues: 54.8277 Evaluate side-chains 165 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.173938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145134 restraints weight = 10866.528| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.05 r_work: 0.3445 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10609 Z= 0.147 Angle : 0.508 5.866 14421 Z= 0.256 Chirality : 0.041 0.140 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.774 19.510 1421 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.36 % Allowed : 8.70 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1319 helix: 1.67 (0.18), residues: 892 sheet: -1.30 (0.58), residues: 54 loop : 1.17 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 80 HIS 0.002 0.001 HIS F 12 PHE 0.013 0.001 PHE C 32 TYR 0.013 0.001 TYR F 169 ARG 0.002 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 639) hydrogen bonds : angle 3.72761 ( 1887) covalent geometry : bond 0.00373 (10609) covalent geometry : angle 0.50831 (14421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4376.98 seconds wall clock time: 76 minutes 55.47 seconds (4615.47 seconds total)