Starting phenix.real_space_refine on Mon Dec 30 05:58:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl0_16708/12_2024/8cl0_16708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl0_16708/12_2024/8cl0_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_16708/12_2024/8cl0_16708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl0_16708/12_2024/8cl0_16708.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl0_16708/12_2024/8cl0_16708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl0_16708/12_2024/8cl0_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-5532/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: 8.06, per 1000 atoms: 0.78 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: 3.00 Conformation dependent library (CDL) restraints added in 1.3 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: 1.03 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: 2.75 Time building geometry restraints manager: 3.40 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.660 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- 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= 0.351 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 *********************** 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 : 1.153 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: 0.2378 time to fit residues: 73.6483 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 : 1.227 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 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= 0.326 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 *********************** 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 : 1.259 Fit side-chains REVERT: B 187 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: C 75 GLU cc_start: 0.7156 (tt0) cc_final: 0.6919 (tt0) REVERT: C 108 THR cc_start: 0.8738 (p) cc_final: 0.8528 (m) REVERT: C 140 LYS cc_start: 0.8351 (mttt) cc_final: 0.8117 (mttp) REVERT: D 39 MET cc_start: 0.7842 (tpt) cc_final: 0.7514 (tpt) REVERT: E 103 ASP cc_start: 0.7716 (m-30) cc_final: 0.7471 (m-30) REVERT: E 113 GLU cc_start: 0.7954 (mp0) cc_final: 0.7633 (mp0) outliers start: 16 outliers final: 9 residues processed: 188 average time/residue: 0.2524 time to fit residues: 65.4520 Evaluate side-chains 177 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 66 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 0.0370 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10609 Z= 0.246 Angle : 0.507 5.686 14421 Z= 0.259 Chirality : 0.041 0.152 1639 Planarity : 0.004 0.032 1867 Dihedral : 4.356 45.821 1424 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.63 % Allowed : 4.80 % 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: 1.78 (0.22), residues: 1319 helix: 1.45 (0.17), residues: 882 sheet: -0.96 (1.76), residues: 9 loop : 0.91 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 184 HIS 0.003 0.001 HIS D 84 PHE 0.015 0.002 PHE E 32 TYR 0.016 0.001 TYR F 169 ARG 0.003 0.000 ARG D 97 *********************** 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 187 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.141 Fit side-chains REVERT: B 187 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: C 66 MET cc_start: 0.8493 (mmm) cc_final: 0.8059 (mmp) REVERT: C 75 GLU cc_start: 0.7153 (tt0) cc_final: 0.6918 (tt0) REVERT: C 108 THR cc_start: 0.8796 (p) cc_final: 0.8542 (m) REVERT: C 140 LYS cc_start: 0.8360 (mttt) cc_final: 0.8144 (mtpp) REVERT: E 68 MET cc_start: 0.8315 (mtm) cc_final: 0.8103 (mtt) REVERT: E 103 ASP cc_start: 0.7653 (m-30) cc_final: 0.7393 (m-30) REVERT: E 113 GLU cc_start: 0.7948 (mp0) cc_final: 0.7702 (mp0) REVERT: E 180 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6508 (mm-30) REVERT: E 215 MET cc_start: 0.8129 (mtp) cc_final: 0.7590 (mtp) REVERT: F 172 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7942 (tp) outliers start: 18 outliers final: 7 residues processed: 179 average time/residue: 0.2608 time to fit residues: 63.8814 Evaluate side-chains 168 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 127 optimal weight: 0.1980 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 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 D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10609 Z= 0.236 Angle : 0.494 5.433 14421 Z= 0.251 Chirality : 0.041 0.156 1639 Planarity : 0.004 0.036 1867 Dihedral : 3.962 20.066 1421 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.36 % Allowed : 5.80 % Favored : 92.84 % 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: 1.88 (0.23), residues: 1319 helix: 1.61 (0.17), residues: 882 sheet: -1.47 (0.62), residues: 45 loop : 0.99 (0.30), residues: 392 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 0.013 0.002 PHE E 32 TYR 0.016 0.001 TYR F 169 ARG 0.002 0.000 ARG B 97 *********************** 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 184 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.114 Fit side-chains REVERT: C 66 MET cc_start: 0.8503 (mmm) cc_final: 0.8035 (mmp) REVERT: C 75 GLU cc_start: 0.7241 (tt0) cc_final: 0.6906 (tt0) REVERT: C 108 THR cc_start: 0.8867 (p) cc_final: 0.8576 (m) REVERT: C 140 LYS cc_start: 0.8359 (mttt) cc_final: 0.8107 (mtpp) REVERT: D 39 MET cc_start: 0.7816 (tpt) cc_final: 0.7551 (tpt) REVERT: E 30 LYS cc_start: 0.8261 (mttt) cc_final: 0.7968 (mttt) REVERT: E 103 ASP cc_start: 0.7684 (m-30) cc_final: 0.7400 (m-30) REVERT: E 180 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6633 (mm-30) REVERT: E 215 MET cc_start: 0.8134 (mtp) cc_final: 0.7622 (mtp) outliers start: 15 outliers final: 9 residues processed: 176 average time/residue: 0.2572 time to fit residues: 62.2151 Evaluate side-chains 167 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET 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 72 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 0.0970 chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2762 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= 0.280 Angle : 0.512 6.086 14421 Z= 0.259 Chirality : 0.042 0.151 1639 Planarity : 0.004 0.036 1867 Dihedral : 3.988 20.181 1421 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.27 % Allowed : 6.79 % Favored : 91.94 % 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: 1.86 (0.23), residues: 1319 helix: 1.57 (0.18), residues: 882 sheet: -1.41 (0.62), residues: 45 loop : 1.05 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 80 HIS 0.003 0.001 HIS D 84 PHE 0.014 0.002 PHE E 32 TYR 0.016 0.001 TYR F 169 ARG 0.002 0.000 ARG F 82 *********************** 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 172 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.215 Fit side-chains REVERT: A 167 ARG cc_start: 0.8191 (mtp180) cc_final: 0.7904 (mtp180) REVERT: B 187 GLU cc_start: 0.7255 (mp0) cc_final: 0.6974 (mp0) REVERT: C 75 GLU cc_start: 0.7283 (tt0) cc_final: 0.6943 (tt0) REVERT: C 108 THR cc_start: 0.8929 (p) cc_final: 0.8635 (m) REVERT: C 140 LYS cc_start: 0.8348 (mttt) cc_final: 0.8086 (mtpp) REVERT: D 39 MET cc_start: 0.7927 (tpt) cc_final: 0.7553 (tpt) REVERT: E 103 ASP cc_start: 0.7714 (m-30) cc_final: 0.7448 (m-30) REVERT: F 172 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7956 (tp) outliers start: 14 outliers final: 10 residues processed: 165 average time/residue: 0.2676 time to fit residues: 60.2367 Evaluate side-chains 166 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 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 114 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 127 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 123 optimal weight: 0.7980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS C 63 GLN D 219 GLN F 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2994 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= 0.165 Angle : 0.458 5.498 14421 Z= 0.232 Chirality : 0.040 0.144 1639 Planarity : 0.004 0.037 1867 Dihedral : 3.702 18.228 1421 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.09 % Allowed : 7.25 % Favored : 91.67 % 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: 2.08 (0.23), residues: 1319 helix: 1.75 (0.18), residues: 886 sheet: -1.33 (0.63), residues: 45 loop : 1.10 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.002 0.000 HIS F 84 PHE 0.013 0.001 PHE C 32 TYR 0.012 0.001 TYR F 169 ARG 0.002 0.000 ARG E 143 *********************** 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 173 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.280 Fit side-chains REVERT: B 76 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 187 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: C 75 GLU cc_start: 0.7256 (tt0) cc_final: 0.7017 (tt0) REVERT: C 108 THR cc_start: 0.8901 (p) cc_final: 0.8557 (m) REVERT: C 140 LYS cc_start: 0.8346 (mttt) cc_final: 0.8096 (mtpp) REVERT: C 214 MET cc_start: 0.8357 (mtp) cc_final: 0.8116 (mtp) REVERT: D 39 MET cc_start: 0.7848 (tpt) cc_final: 0.7640 (tpp) REVERT: E 103 ASP cc_start: 0.7663 (m-30) cc_final: 0.7383 (m-30) outliers start: 12 outliers final: 8 residues processed: 168 average time/residue: 0.2572 time to fit residues: 59.1421 Evaluate side-chains 162 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 F residue 35 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 107 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 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 B 219 GLN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3033 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= 0.209 Angle : 0.475 6.320 14421 Z= 0.240 Chirality : 0.040 0.139 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.704 18.248 1421 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.27 % Allowed : 7.61 % 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: 2.05 (0.23), residues: 1319 helix: 1.73 (0.18), residues: 886 sheet: -1.43 (0.57), residues: 54 loop : 1.16 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 80 HIS 0.002 0.000 HIS C 62 PHE 0.013 0.001 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.002 0.000 ARG C 143 *********************** 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 171 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.206 Fit side-chains REVERT: A 167 ARG cc_start: 0.8177 (mtp180) cc_final: 0.7944 (mtp180) REVERT: B 76 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 187 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: C 75 GLU cc_start: 0.7272 (tt0) cc_final: 0.7032 (tt0) REVERT: C 108 THR cc_start: 0.8956 (p) cc_final: 0.8634 (m) REVERT: C 140 LYS cc_start: 0.8336 (mttt) cc_final: 0.8073 (mtpp) REVERT: C 214 MET cc_start: 0.8344 (mtp) cc_final: 0.8125 (mtp) REVERT: D 39 MET cc_start: 0.7840 (tpt) cc_final: 0.7605 (tpp) REVERT: E 103 ASP cc_start: 0.7691 (m-30) cc_final: 0.7407 (m-30) REVERT: F 154 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7456 (mtp180) outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 0.2679 time to fit residues: 60.1908 Evaluate side-chains 162 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.3980 chunk 111 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3078 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= 0.222 Angle : 0.483 6.487 14421 Z= 0.243 Chirality : 0.041 0.139 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.726 18.308 1421 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.27 % Allowed : 8.15 % 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 (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: 2.01 (0.23), residues: 1319 helix: 1.69 (0.17), residues: 891 sheet: -1.40 (0.57), residues: 54 loop : 1.15 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 80 HIS 0.002 0.000 HIS D 84 PHE 0.013 0.001 PHE E 32 TYR 0.014 0.001 TYR F 169 ARG 0.003 0.000 ARG B 143 *********************** 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 178 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: B 76 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 187 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: C 75 GLU cc_start: 0.7279 (tt0) cc_final: 0.7042 (tt0) REVERT: C 108 THR cc_start: 0.8944 (p) cc_final: 0.8646 (m) REVERT: C 140 LYS cc_start: 0.8319 (mttt) cc_final: 0.8074 (mtpp) REVERT: C 214 MET cc_start: 0.8346 (mtp) cc_final: 0.8119 (mtp) REVERT: D 39 MET cc_start: 0.7872 (tpt) cc_final: 0.7615 (tpp) REVERT: E 103 ASP cc_start: 0.7691 (m-30) cc_final: 0.7393 (m-30) REVERT: F 154 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7460 (mtp180) outliers start: 14 outliers final: 11 residues processed: 169 average time/residue: 0.2578 time to fit residues: 59.9091 Evaluate side-chains 167 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3121 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= 0.223 Angle : 0.492 7.128 14421 Z= 0.248 Chirality : 0.041 0.139 1639 Planarity : 0.004 0.039 1867 Dihedral : 3.720 18.240 1421 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.18 % Allowed : 8.70 % Favored : 90.13 % 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: 2.01 (0.23), residues: 1319 helix: 1.69 (0.18), residues: 891 sheet: -1.32 (0.58), residues: 54 loop : 1.13 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 80 HIS 0.002 0.000 HIS C 62 PHE 0.013 0.001 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.004 0.000 ARG B 143 *********************** 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 167 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.210 Fit side-chains REVERT: B 76 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7636 (mm-30) REVERT: B 187 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: C 75 GLU cc_start: 0.7290 (tt0) cc_final: 0.7033 (tt0) REVERT: C 108 THR cc_start: 0.8974 (p) cc_final: 0.8665 (m) REVERT: C 140 LYS cc_start: 0.8314 (mttt) cc_final: 0.8068 (mtpp) REVERT: C 214 MET cc_start: 0.8355 (mtp) cc_final: 0.8145 (mtp) REVERT: D 39 MET cc_start: 0.7871 (tpt) cc_final: 0.7611 (tpp) REVERT: E 103 ASP cc_start: 0.7687 (m-30) cc_final: 0.7394 (m-30) REVERT: E 215 MET cc_start: 0.7580 (mtp) cc_final: 0.7185 (mtp) REVERT: F 154 ARG cc_start: 0.7868 (mtp-110) cc_final: 0.7449 (mtp180) outliers start: 13 outliers final: 10 residues processed: 159 average time/residue: 0.2790 time to fit residues: 60.3477 Evaluate side-chains 162 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 0.0980 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3244 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= 0.184 Angle : 0.477 6.565 14421 Z= 0.241 Chirality : 0.040 0.136 1639 Planarity : 0.004 0.039 1867 Dihedral : 3.624 17.059 1421 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.09 % Allowed : 8.70 % Favored : 90.22 % 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: 2.12 (0.23), residues: 1319 helix: 1.78 (0.18), residues: 892 sheet: -1.29 (0.58), residues: 54 loop : 1.15 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 80 HIS 0.001 0.000 HIS D 84 PHE 0.015 0.001 PHE F 32 TYR 0.013 0.001 TYR F 169 ARG 0.003 0.000 ARG B 143 ********************** 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 159 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: B 76 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 187 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: C 75 GLU cc_start: 0.7289 (tt0) cc_final: 0.7053 (tt0) REVERT: C 140 LYS cc_start: 0.8298 (mttt) cc_final: 0.8067 (mtpp) REVERT: D 39 MET cc_start: 0.7841 (tpt) cc_final: 0.7243 (tpt) REVERT: E 103 ASP cc_start: 0.7647 (m-30) cc_final: 0.7347 (m-30) REVERT: E 215 MET cc_start: 0.7537 (mtp) cc_final: 0.7163 (mtp) REVERT: F 143 ARG cc_start: 0.7498 (ttp-170) cc_final: 0.7295 (ttp80) REVERT: F 154 ARG cc_start: 0.7839 (mtp-110) cc_final: 0.7423 (mtp180) outliers start: 12 outliers final: 9 residues processed: 153 average time/residue: 0.2577 time to fit residues: 53.9470 Evaluate side-chains 154 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.176131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147237 restraints weight = 10834.661| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.05 r_work: 0.3470 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3259 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= 0.199 Angle : 0.486 6.454 14421 Z= 0.245 Chirality : 0.040 0.136 1639 Planarity : 0.004 0.039 1867 Dihedral : 3.637 17.382 1421 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.00 % Allowed : 8.79 % Favored : 90.22 % 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: 2.10 (0.23), residues: 1319 helix: 1.77 (0.17), residues: 892 sheet: -1.26 (0.59), residues: 54 loop : 1.14 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 80 HIS 0.002 0.000 HIS D 84 PHE 0.012 0.001 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.003 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2332.73 seconds wall clock time: 43 minutes 31.38 seconds (2611.38 seconds total)