Starting phenix.real_space_refine on Sat Aug 23 13:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl0_16708/08_2025/8cl0_16708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl0_16708/08_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_16708/08_2025/8cl0_16708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl0_16708/08_2025/8cl0_16708.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl0_16708/08_2025/8cl0_16708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl0_16708/08_2025/8cl0_16708.cif" } resolution = 3.12 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= 0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU: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: {'ASN:plan1': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU: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, 'HIS:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 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: {'ASN:plan1': 2, 'GLN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP: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, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP: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: {'ASN:plan1': 2, 'GLN:plan1': 3, 'HIS:plan': 1, 'GLU: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: 2.32, per 1000 atoms: 0.22 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: 0.84 Conformation dependent library (CDL) restraints added in 264.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.30 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: 1.49 Time building geometry restraints manager: 1.09 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: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.530 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.027 0.003 ARG B 154 TYR 0.027 0.006 TYR C 169 PHE 0.012 0.003 PHE H1417 TRP 0.017 0.003 TRP A 117 HIS 0.014 0.003 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00543 (10609) covalent geometry : angle 0.86933 (14421) hydrogen bonds : bond 0.10258 ( 639) hydrogen bonds : angle 5.95054 ( 1887) *********************** 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 : 0.254 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: 0.0940 time to fit residues: 29.7312 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 : 0.389 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 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 ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.178562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151791 restraints weight = 10882.843| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.87 r_work: 0.3474 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10609 Z= 0.162 Angle : 0.549 6.113 14421 Z= 0.285 Chirality : 0.042 0.165 1639 Planarity : 0.005 0.032 1867 Dihedral : 4.935 54.383 1427 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.45 % Allowed : 4.08 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 1.38 (0.22), residues: 1319 helix: 1.17 (0.17), residues: 882 sheet: -1.95 (0.54), residues: 45 loop : 1.01 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 143 TYR 0.018 0.001 TYR F 169 PHE 0.015 0.002 PHE A 32 TRP 0.010 0.001 TRP C 117 HIS 0.003 0.001 HIS F 120 Details of bonding type rmsd covalent geometry : bond 0.00405 (10609) covalent geometry : angle 0.54884 (14421) hydrogen bonds : bond 0.03982 ( 639) hydrogen bonds : angle 4.15554 ( 1887) *********************** 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 199 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.308 Fit side-chains REVERT: A 79 GLU cc_start: 0.7785 (tt0) cc_final: 0.7354 (tp30) REVERT: B 159 GLU cc_start: 0.7908 (tt0) cc_final: 0.7700 (tt0) REVERT: B 187 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: C 75 GLU cc_start: 0.7874 (tt0) cc_final: 0.7563 (tt0) REVERT: C 108 THR cc_start: 0.8881 (p) cc_final: 0.8653 (m) REVERT: C 140 LYS cc_start: 0.8746 (mttt) cc_final: 0.8428 (mttp) REVERT: D 39 MET cc_start: 0.8428 (tpt) cc_final: 0.8177 (tpt) REVERT: D 54 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8390 (m) REVERT: D 219 GLN cc_start: 0.6562 (tt0) cc_final: 0.6344 (tt0) REVERT: E 68 MET cc_start: 0.8484 (mtm) cc_final: 0.8103 (mtt) REVERT: E 103 ASP cc_start: 0.7906 (m-30) cc_final: 0.7670 (m-30) REVERT: E 113 GLU cc_start: 0.8185 (mp0) cc_final: 0.7569 (mp0) REVERT: E 215 MET cc_start: 0.8114 (mtp) cc_final: 0.7789 (mtp) outliers start: 16 outliers final: 9 residues processed: 189 average time/residue: 0.0929 time to fit residues: 24.4954 Evaluate side-chains 177 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 54 THR 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 22 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.169620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.140161 restraints weight = 10961.350| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.08 r_work: 0.3422 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10609 Z= 0.165 Angle : 0.520 5.918 14421 Z= 0.264 Chirality : 0.042 0.152 1639 Planarity : 0.005 0.032 1867 Dihedral : 4.351 44.587 1424 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.45 % Allowed : 4.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.22), residues: 1319 helix: 1.48 (0.17), residues: 882 sheet: -1.00 (1.75), residues: 9 loop : 0.91 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 143 TYR 0.017 0.001 TYR F 169 PHE 0.014 0.002 PHE E 32 TRP 0.008 0.001 TRP F 184 HIS 0.003 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00418 (10609) covalent geometry : angle 0.52019 (14421) hydrogen bonds : bond 0.03720 ( 639) hydrogen bonds : angle 3.89280 ( 1887) *********************** 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 184 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.406 Fit side-chains REVERT: B 159 GLU cc_start: 0.7973 (tt0) cc_final: 0.7734 (tt0) REVERT: B 187 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: C 66 MET cc_start: 0.8783 (mmm) cc_final: 0.8390 (mmp) REVERT: C 140 LYS cc_start: 0.8699 (mttt) cc_final: 0.8440 (mtpp) REVERT: E 113 GLU cc_start: 0.8255 (mp0) cc_final: 0.7482 (mp0) REVERT: E 215 MET cc_start: 0.8070 (mtp) cc_final: 0.7516 (mtp) outliers start: 16 outliers final: 8 residues processed: 177 average time/residue: 0.1070 time to fit residues: 26.0693 Evaluate side-chains 165 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 98 optimal weight: 0.0470 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.177166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149855 restraints weight = 10917.062| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.89 r_work: 0.3452 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10609 Z= 0.140 Angle : 0.494 5.530 14421 Z= 0.251 Chirality : 0.041 0.162 1639 Planarity : 0.004 0.036 1867 Dihedral : 3.951 20.097 1421 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.27 % Allowed : 5.98 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 1.92 (0.23), residues: 1319 helix: 1.64 (0.17), residues: 882 sheet: -1.46 (0.61), residues: 45 loop : 1.00 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 143 TYR 0.015 0.001 TYR F 169 PHE 0.013 0.001 PHE E 32 TRP 0.006 0.001 TRP F 184 HIS 0.003 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00351 (10609) covalent geometry : angle 0.49431 (14421) hydrogen bonds : bond 0.03471 ( 639) hydrogen bonds : angle 3.77366 ( 1887) *********************** 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 178 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.459 Fit side-chains REVERT: B 187 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: C 66 MET cc_start: 0.8795 (mmm) cc_final: 0.8357 (mmp) REVERT: C 75 GLU cc_start: 0.8023 (tt0) cc_final: 0.7721 (tt0) REVERT: C 140 LYS cc_start: 0.8741 (mttt) cc_final: 0.8463 (mtpp) REVERT: E 113 GLU cc_start: 0.8241 (mp0) cc_final: 0.7648 (mp0) REVERT: E 180 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6627 (mm-30) REVERT: E 215 MET cc_start: 0.8074 (mtp) cc_final: 0.7480 (mtp) REVERT: F 172 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8129 (tp) outliers start: 14 outliers final: 8 residues processed: 171 average time/residue: 0.1015 time to fit residues: 24.0660 Evaluate side-chains 163 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 113 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 36 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 193 ASN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.178459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.151271 restraints weight = 10858.792| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.88 r_work: 0.3474 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10609 Z= 0.126 Angle : 0.480 6.252 14421 Z= 0.243 Chirality : 0.041 0.145 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.785 18.208 1421 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.18 % Allowed : 6.43 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 2.07 (0.23), residues: 1319 helix: 1.75 (0.18), residues: 882 sheet: -1.24 (0.63), residues: 45 loop : 1.06 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 143 TYR 0.013 0.001 TYR F 169 PHE 0.012 0.001 PHE E 32 TRP 0.007 0.001 TRP F 184 HIS 0.002 0.000 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00315 (10609) covalent geometry : angle 0.48049 (14421) hydrogen bonds : bond 0.03345 ( 639) hydrogen bonds : angle 3.69100 ( 1887) *********************** 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 176 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.424 Fit side-chains REVERT: A 167 ARG cc_start: 0.8366 (mtp180) cc_final: 0.8120 (mtp180) REVERT: B 187 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: C 66 MET cc_start: 0.8769 (mmm) cc_final: 0.8324 (mmp) REVERT: C 75 GLU cc_start: 0.8025 (tt0) cc_final: 0.7698 (tt0) REVERT: C 140 LYS cc_start: 0.8711 (mttt) cc_final: 0.8417 (mtpp) REVERT: E 215 MET cc_start: 0.8104 (mtp) cc_final: 0.7528 (mtp) REVERT: F 45 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7456 (mm-30) REVERT: F 172 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8131 (tp) outliers start: 13 outliers final: 8 residues processed: 171 average time/residue: 0.1154 time to fit residues: 27.0678 Evaluate side-chains 161 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR 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 10 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 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 = 0.3846 r_free = 0.3846 target = 0.165815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135989 restraints weight = 11107.097| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.11 r_work: 0.3417 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10609 Z= 0.178 Angle : 0.520 6.935 14421 Z= 0.261 Chirality : 0.042 0.144 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.935 19.739 1421 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.27 % Allowed : 7.34 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 1.92 (0.23), residues: 1319 helix: 1.60 (0.18), residues: 886 sheet: -1.22 (0.63), residues: 45 loop : 1.08 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 143 TYR 0.016 0.002 TYR F 169 PHE 0.014 0.002 PHE E 32 TRP 0.008 0.001 TRP B 80 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00454 (10609) covalent geometry : angle 0.52026 (14421) hydrogen bonds : bond 0.03631 ( 639) hydrogen bonds : angle 3.76993 ( 1887) *********************** 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: 14 poor density : 168 time to evaluate : 0.424 Fit side-chains REVERT: B 76 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7871 (mm-30) REVERT: B 187 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: C 25 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8112 (mtpt) REVERT: C 75 GLU cc_start: 0.7998 (tt0) cc_final: 0.7669 (tt0) REVERT: C 140 LYS cc_start: 0.8677 (mttt) cc_final: 0.8321 (mtpp) REVERT: D 39 MET cc_start: 0.8245 (tpp) cc_final: 0.8004 (tpt) REVERT: E 113 GLU cc_start: 0.8241 (mp0) cc_final: 0.7509 (mp0) REVERT: E 144 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8340 (ttm) REVERT: F 45 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7406 (mm-30) REVERT: F 172 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7977 (tp) outliers start: 14 outliers final: 9 residues processed: 174 average time/residue: 0.1217 time to fit residues: 28.9552 Evaluate side-chains 173 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 E residue 144 MET 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 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 108 optimal weight: 2.9990 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 ** A 193 ASN ** 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 = 0.3956 r_free = 0.3956 target = 0.175073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146240 restraints weight = 10844.389| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.04 r_work: 0.3459 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 0.036 10609 Z= 0.126 Angle : 0.484 5.933 14421 Z= 0.244 Chirality : 0.040 0.140 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.762 19.061 1421 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.27 % Allowed : 7.70 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.23), residues: 1319 helix: 1.72 (0.18), residues: 886 sheet: -1.18 (0.64), residues: 45 loop : 1.09 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 143 TYR 0.013 0.001 TYR F 169 PHE 0.014 0.001 PHE C 32 TRP 0.006 0.001 TRP F 184 HIS 0.002 0.000 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00315 (10609) covalent geometry : angle 0.48356 (14421) hydrogen bonds : bond 0.03344 ( 639) hydrogen bonds : angle 3.67643 ( 1887) *********************** 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 181 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.393 Fit side-chains REVERT: A 167 ARG cc_start: 0.8262 (mtp180) cc_final: 0.8039 (mtp180) REVERT: B 76 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 187 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: C 25 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7766 (mtpp) REVERT: C 75 GLU cc_start: 0.7990 (tt0) cc_final: 0.7678 (tt0) REVERT: C 140 LYS cc_start: 0.8685 (mttt) cc_final: 0.8341 (mtpp) REVERT: D 39 MET cc_start: 0.8238 (tpp) cc_final: 0.8006 (tpt) REVERT: E 113 GLU cc_start: 0.8229 (mp0) cc_final: 0.7627 (mp0) REVERT: E 215 MET cc_start: 0.8072 (mtp) cc_final: 0.7529 (mtp) REVERT: F 45 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7421 (mm-30) REVERT: F 154 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7572 (mtp180) REVERT: F 172 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8008 (tp) outliers start: 14 outliers final: 9 residues processed: 172 average time/residue: 0.1101 time to fit residues: 26.0649 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 : 0.369 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 46 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 79 optimal weight: 0.0030 chunk 116 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3938 r_free = 0.3938 target = 0.173023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145486 restraints weight = 10927.192| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.92 r_work: 0.3447 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3020 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= 0.149 Angle : 0.505 5.842 14421 Z= 0.254 Chirality : 0.041 0.141 1639 Planarity : 0.004 0.040 1867 Dihedral : 3.789 19.322 1421 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.18 % Allowed : 8.06 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 2.00 (0.23), residues: 1319 helix: 1.67 (0.18), residues: 886 sheet: -1.15 (0.64), residues: 45 loop : 1.09 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 143 TYR 0.014 0.001 TYR F 169 PHE 0.014 0.001 PHE E 32 TRP 0.008 0.001 TRP B 80 HIS 0.002 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00376 (10609) covalent geometry : angle 0.50463 (14421) hydrogen bonds : bond 0.03470 ( 639) hydrogen bonds : angle 3.71948 ( 1887) *********************** 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 173 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7526 (tp30) cc_final: 0.7254 (tp30) REVERT: B 76 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7943 (mm-30) REVERT: B 187 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: C 25 LYS cc_start: 0.8384 (mtpt) cc_final: 0.7890 (mtpp) REVERT: C 75 GLU cc_start: 0.8103 (tt0) cc_final: 0.7803 (tt0) REVERT: C 140 LYS cc_start: 0.8742 (mttt) cc_final: 0.8431 (mtpp) REVERT: D 39 MET cc_start: 0.8305 (tpp) cc_final: 0.8071 (tpt) REVERT: E 113 GLU cc_start: 0.8250 (mp0) cc_final: 0.7718 (mp0) REVERT: E 144 MET cc_start: 0.8653 (ttm) cc_final: 0.8445 (ttm) REVERT: F 45 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7492 (mm-30) REVERT: F 154 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7638 (mtp180) REVERT: F 172 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8122 (tp) outliers start: 13 outliers final: 10 residues processed: 166 average time/residue: 0.1205 time to fit residues: 27.0737 Evaluate side-chains 171 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 191 VAL 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 131 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 113 optimal weight: 0.1980 chunk 107 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 92 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 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 = 0.3968 r_free = 0.3968 target = 0.176177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147691 restraints weight = 10761.702| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.01 r_work: 0.3483 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3206 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= 0.111 Angle : 0.481 8.010 14421 Z= 0.242 Chirality : 0.040 0.144 1639 Planarity : 0.004 0.039 1867 Dihedral : 3.623 17.549 1421 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.18 % Allowed : 8.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.23), residues: 1319 helix: 1.81 (0.18), residues: 891 sheet: -1.13 (0.65), residues: 45 loop : 1.08 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 143 TYR 0.012 0.001 TYR F 169 PHE 0.012 0.001 PHE E 32 TRP 0.006 0.001 TRP B 133 HIS 0.001 0.000 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00270 (10609) covalent geometry : angle 0.48068 (14421) hydrogen bonds : bond 0.03230 ( 639) hydrogen bonds : angle 3.65923 ( 1887) *********************** 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 170 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7532 (tp30) cc_final: 0.7210 (tp30) REVERT: B 76 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7838 (mm-30) REVERT: B 187 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: C 25 LYS cc_start: 0.8277 (mtpt) cc_final: 0.7781 (mtpp) REVERT: C 71 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7735 (pt0) REVERT: C 75 GLU cc_start: 0.8005 (tt0) cc_final: 0.7478 (pt0) REVERT: C 140 LYS cc_start: 0.8668 (mttt) cc_final: 0.8362 (mtpp) REVERT: D 39 MET cc_start: 0.8168 (tpp) cc_final: 0.7916 (tpt) REVERT: E 144 MET cc_start: 0.8531 (ttm) cc_final: 0.8265 (ttm) REVERT: E 215 MET cc_start: 0.8061 (mtp) cc_final: 0.7543 (mtp) REVERT: F 45 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7322 (mm-30) REVERT: F 154 ARG cc_start: 0.7940 (mtp-110) cc_final: 0.7536 (mtp180) REVERT: F 172 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.8003 (tp) outliers start: 13 outliers final: 9 residues processed: 164 average time/residue: 0.1209 time to fit residues: 27.1488 Evaluate side-chains 164 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 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 11 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 115 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 193 ASN ** 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 = 0.4005 r_free = 0.4005 target = 0.179752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.152686 restraints weight = 10788.146| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.87 r_work: 0.3491 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3233 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= 0.118 Angle : 0.488 8.229 14421 Z= 0.246 Chirality : 0.040 0.161 1639 Planarity : 0.004 0.039 1867 Dihedral : 3.611 17.297 1421 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.18 % Allowed : 8.24 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.23), residues: 1319 helix: 1.84 (0.18), residues: 891 sheet: -1.29 (0.59), residues: 54 loop : 1.11 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 143 TYR 0.013 0.001 TYR F 169 PHE 0.013 0.001 PHE F 32 TRP 0.006 0.001 TRP B 80 HIS 0.002 0.000 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00289 (10609) covalent geometry : angle 0.48804 (14421) hydrogen bonds : bond 0.03250 ( 639) hydrogen bonds : angle 3.66574 ( 1887) ********************** 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 168 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7513 (tp30) cc_final: 0.7221 (tp30) REVERT: B 76 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7901 (mm-30) REVERT: B 187 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: C 25 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7820 (mtpp) REVERT: C 29 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7829 (pt0) REVERT: C 75 GLU cc_start: 0.8076 (tt0) cc_final: 0.7575 (pt0) REVERT: C 140 LYS cc_start: 0.8696 (mttt) cc_final: 0.8432 (mtpp) REVERT: D 39 MET cc_start: 0.8229 (tpp) cc_final: 0.7962 (tpt) REVERT: D 66 MET cc_start: 0.8093 (mmt) cc_final: 0.7771 (mmt) REVERT: E 144 MET cc_start: 0.8527 (ttm) cc_final: 0.8234 (ttm) REVERT: E 215 MET cc_start: 0.8108 (mtp) cc_final: 0.7592 (mtp) REVERT: F 154 ARG cc_start: 0.7984 (mtp-110) cc_final: 0.7582 (mtp180) REVERT: F 172 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8112 (tp) outliers start: 13 outliers final: 9 residues processed: 163 average time/residue: 0.0948 time to fit residues: 21.2563 Evaluate side-chains 161 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 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 11 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 193 ASN ** 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 = 0.3867 r_free = 0.3867 target = 0.167750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138271 restraints weight = 11061.224| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.07 r_work: 0.3448 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3196 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 : 0.510 8.076 14421 Z= 0.256 Chirality : 0.041 0.163 1639 Planarity : 0.004 0.040 1867 Dihedral : 3.717 18.309 1421 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.18 % Allowed : 8.33 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 2.07 (0.23), residues: 1319 helix: 1.77 (0.18), residues: 891 sheet: -1.27 (0.59), residues: 54 loop : 1.06 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 143 TYR 0.014 0.001 TYR F 169 PHE 0.013 0.001 PHE E 32 TRP 0.008 0.001 TRP B 80 HIS 0.002 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00359 (10609) covalent geometry : angle 0.50974 (14421) hydrogen bonds : bond 0.03419 ( 639) hydrogen bonds : angle 3.70743 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.31 seconds wall clock time: 37 minutes 9.68 seconds (2229.68 seconds total)