Starting phenix.real_space_refine on Fri Mar 15 22:27:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl0_16708/03_2024/8cl0_16708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl0_16708/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl0_16708/03_2024/8cl0_16708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl0_16708/03_2024/8cl0_16708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl0_16708/03_2024/8cl0_16708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl0_16708/03_2024/8cl0_16708.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.32, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 3.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 6 sheets defined 69.2% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 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: 2.38 Time building geometry restraints manager: 3.86 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: 96.62 - 104.13: 283 104.13 - 111.63: 4419 111.63 - 119.14: 4400 119.14 - 126.64: 5110 126.64 - 134.15: 209 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 2.440 nonbonded pdb=" NH1 ARG E 143 " pdb=" O ASN L1409 " model vdw 2.372 2.520 nonbonded pdb=" OG SER D 33 " pdb=" OE1 GLU D 35 " model vdw 2.437 2.440 nonbonded pdb=" OG SER C 33 " pdb=" OE1 GLU C 35 " model vdw 2.480 2.440 nonbonded pdb=" O THR A 54 " pdb=" OG1 THR A 58 " model vdw 2.481 2.440 ... (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 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 12.160 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 26.560 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.360 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 1.359 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: 0.2434 time to fit residues: 75.6797 Evaluate side-chains 172 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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: 0.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7403 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10609 Z= 0.311 Angle : 0.567 6.498 14421 Z= 0.292 Chirality : 0.043 0.168 1639 Planarity : 0.005 0.033 1867 Dihedral : 4.900 52.038 1427 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.63 % Allowed : 4.08 % Favored : 94.29 % 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: 1.28 (0.22), residues: 1319 helix: 1.09 (0.17), residues: 879 sheet: -1.95 (0.54), residues: 45 loop : 0.97 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 117 HIS 0.004 0.001 HIS F 120 PHE 0.015 0.002 PHE A 32 TYR 0.019 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 195 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.106 Fit side-chains REVERT: C 75 GLU cc_start: 0.7136 (tt0) cc_final: 0.6907 (tt0) REVERT: C 140 LYS cc_start: 0.8367 (mttt) cc_final: 0.8135 (mttp) REVERT: D 39 MET cc_start: 0.7840 (tpt) cc_final: 0.7524 (tpt) REVERT: D 54 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8135 (m) REVERT: E 68 MET cc_start: 0.8152 (mtm) cc_final: 0.7804 (mtt) REVERT: E 103 ASP cc_start: 0.7721 (m-30) cc_final: 0.7460 (m-30) REVERT: E 113 GLU cc_start: 0.7902 (mp0) cc_final: 0.7632 (mp0) REVERT: E 180 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6463 (mm-30) REVERT: E 215 MET cc_start: 0.8174 (mtp) cc_final: 0.7877 (mtp) outliers start: 18 outliers final: 10 residues processed: 186 average time/residue: 0.2565 time to fit residues: 64.8081 Evaluate side-chains 172 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 197 ASP 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 D residue 216 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: 0.0970 chunk 99 optimal weight: 0.0040 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 96 optimal weight: 0.9980 overall best weight: 0.3948 ------------------------------------------------------------------------------- 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: 0.7342 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10609 Z= 0.176 Angle : 0.471 5.347 14421 Z= 0.239 Chirality : 0.039 0.147 1639 Planarity : 0.004 0.030 1867 Dihedral : 4.108 45.325 1424 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.36 % Allowed : 5.16 % Favored : 93.48 % 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: 1.90 (0.23), residues: 1319 helix: 1.64 (0.18), residues: 883 sheet: -1.53 (0.60), residues: 45 loop : 0.99 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 184 HIS 0.002 0.000 HIS F 120 PHE 0.012 0.001 PHE E 32 TYR 0.014 0.001 TYR F 169 ARG 0.002 0.000 ARG A 82 *********************** 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 178 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 1.200 Fit side-chains REVERT: A 167 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7849 (mtp180) REVERT: B 28 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6881 (mm-30) REVERT: C 75 GLU cc_start: 0.7146 (tt0) cc_final: 0.6931 (tt0) REVERT: C 140 LYS cc_start: 0.8336 (mttt) cc_final: 0.8082 (mtpp) REVERT: D 39 MET cc_start: 0.7899 (tpt) cc_final: 0.7570 (tpp) REVERT: D 54 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7916 (m) REVERT: E 215 MET cc_start: 0.8006 (mtp) cc_final: 0.7636 (mtp) REVERT: F 143 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7272 (ttp80) REVERT: F 175 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7459 (mm-30) outliers start: 15 outliers final: 8 residues processed: 173 average time/residue: 0.2465 time to fit residues: 58.2670 Evaluate side-chains 163 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR 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 54 THR 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 118 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 0.0980 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS C 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2636 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= 0.288 Angle : 0.515 5.207 14421 Z= 0.259 Chirality : 0.041 0.161 1639 Planarity : 0.004 0.034 1867 Dihedral : 3.981 20.875 1421 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.45 % Allowed : 5.98 % Favored : 92.57 % 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: 1.84 (0.23), residues: 1319 helix: 1.55 (0.18), residues: 883 sheet: -1.38 (0.62), residues: 45 loop : 1.06 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 23 HIS 0.003 0.001 HIS A 120 PHE 0.014 0.002 PHE C 32 TYR 0.017 0.001 TYR F 169 ARG 0.002 0.000 ARG D 173 *********************** 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 fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.120 Fit side-chains REVERT: A 167 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7814 (mtp180) REVERT: B 187 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: C 66 MET cc_start: 0.8475 (mmm) cc_final: 0.8025 (mmp) REVERT: C 75 GLU cc_start: 0.7227 (tt0) cc_final: 0.6952 (tt0) REVERT: C 140 LYS cc_start: 0.8374 (mttt) cc_final: 0.8090 (mtpp) REVERT: C 179 GLN cc_start: 0.8429 (tp40) cc_final: 0.8224 (tp-100) REVERT: D 39 MET cc_start: 0.7965 (tpt) cc_final: 0.7113 (tpt) REVERT: D 54 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (m) REVERT: E 103 ASP cc_start: 0.7664 (m-30) cc_final: 0.7385 (m-30) REVERT: E 113 GLU cc_start: 0.7902 (mp0) cc_final: 0.7454 (mp0) REVERT: E 215 MET cc_start: 0.8170 (mtp) cc_final: 0.7701 (mtp) outliers start: 16 outliers final: 10 residues processed: 176 average time/residue: 0.2452 time to fit residues: 59.3638 Evaluate side-chains 170 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 205 LEU 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 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 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 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: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 176 GLN D 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10609 Z= 0.358 Angle : 0.546 5.576 14421 Z= 0.275 Chirality : 0.043 0.150 1639 Planarity : 0.005 0.036 1867 Dihedral : 4.129 21.424 1421 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.36 % Allowed : 7.16 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.23), residues: 1319 helix: 1.37 (0.17), residues: 883 sheet: -1.43 (0.61), residues: 45 loop : 1.12 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 23 HIS 0.004 0.001 HIS A 120 PHE 0.014 0.002 PHE C 32 TYR 0.017 0.002 TYR F 169 ARG 0.003 0.000 ARG F 143 *********************** 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 192 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 177 time to evaluate : 1.289 Fit side-chains REVERT: A 167 ARG cc_start: 0.8184 (mtp180) cc_final: 0.7887 (mtp180) REVERT: B 76 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 187 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: C 75 GLU cc_start: 0.7255 (tt0) cc_final: 0.6919 (tt0) REVERT: C 140 LYS cc_start: 0.8360 (mttt) cc_final: 0.8137 (mtpp) REVERT: D 54 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7988 (m) REVERT: E 113 GLU cc_start: 0.7965 (mp0) cc_final: 0.7729 (mp0) REVERT: F 96 MET cc_start: 0.7585 (mtm) cc_final: 0.7315 (mtm) outliers start: 15 outliers final: 10 residues processed: 184 average time/residue: 0.2388 time to fit residues: 60.7204 Evaluate side-chains 173 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 205 LEU 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 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 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 123 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 176 GLN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2914 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= 0.221 Angle : 0.488 5.137 14421 Z= 0.245 Chirality : 0.040 0.150 1639 Planarity : 0.004 0.039 1867 Dihedral : 3.878 19.804 1421 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.54 % Allowed : 7.16 % Favored : 91.30 % 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: 1.90 (0.23), residues: 1319 helix: 1.56 (0.18), residues: 883 sheet: -1.33 (0.62), residues: 45 loop : 1.16 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 184 HIS 0.004 0.001 HIS A 120 PHE 0.014 0.001 PHE C 32 TYR 0.013 0.001 TYR F 169 ARG 0.001 0.000 ARG A 167 *********************** 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 188 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 1.163 Fit side-chains REVERT: A 167 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7898 (mtp180) REVERT: B 76 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 187 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: C 75 GLU cc_start: 0.7245 (tt0) cc_final: 0.6927 (tt0) REVERT: C 140 LYS cc_start: 0.8351 (mttt) cc_final: 0.8072 (mtpp) REVERT: C 179 GLN cc_start: 0.8403 (tp40) cc_final: 0.8031 (tp-100) REVERT: D 39 MET cc_start: 0.7923 (tpt) cc_final: 0.7259 (tpt) REVERT: D 54 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7900 (m) REVERT: E 113 GLU cc_start: 0.7900 (mp0) cc_final: 0.7547 (mp0) REVERT: E 215 MET cc_start: 0.8171 (mtp) cc_final: 0.7714 (mtp) REVERT: F 96 MET cc_start: 0.7556 (mtm) cc_final: 0.7340 (mtm) outliers start: 17 outliers final: 12 residues processed: 182 average time/residue: 0.2308 time to fit residues: 58.0730 Evaluate side-chains 176 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 151 LEU 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 54 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 176 GLN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 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 : 0.004 0.036 10609 Z= 0.237 Angle : 0.497 6.609 14421 Z= 0.249 Chirality : 0.040 0.139 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.802 19.581 1421 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.63 % Allowed : 7.61 % 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 (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: 1.93 (0.23), residues: 1319 helix: 1.58 (0.18), residues: 887 sheet: -1.19 (0.65), residues: 45 loop : 1.18 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 80 HIS 0.004 0.001 HIS A 120 PHE 0.013 0.001 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.002 0.000 ARG F 82 *********************** 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 186 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.234 Fit side-chains REVERT: A 167 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7849 (mtp180) REVERT: A 212 GLU cc_start: 0.7308 (tp30) cc_final: 0.7063 (tp30) REVERT: B 76 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 187 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: C 75 GLU cc_start: 0.7257 (tt0) cc_final: 0.6953 (tt0) REVERT: C 140 LYS cc_start: 0.8370 (mttt) cc_final: 0.8084 (mtpp) REVERT: D 39 MET cc_start: 0.7921 (tpt) cc_final: 0.7293 (tpt) REVERT: D 54 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7869 (m) REVERT: E 113 GLU cc_start: 0.7894 (mp0) cc_final: 0.7564 (mp0) REVERT: F 96 MET cc_start: 0.7491 (mtm) cc_final: 0.7274 (mtm) outliers start: 18 outliers final: 12 residues processed: 180 average time/residue: 0.2376 time to fit residues: 59.0994 Evaluate side-chains 178 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 205 LEU 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 144 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 189 LEU 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: 1.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 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 ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3110 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= 0.202 Angle : 0.490 6.954 14421 Z= 0.244 Chirality : 0.040 0.138 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.697 18.496 1421 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.36 % Allowed : 8.88 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.23), residues: 1319 helix: 1.69 (0.18), residues: 887 sheet: -1.16 (0.65), residues: 45 loop : 1.21 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 80 HIS 0.005 0.001 HIS A 120 PHE 0.014 0.001 PHE F 32 TYR 0.013 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 177 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7820 (mtp180) REVERT: B 76 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7568 (mm-30) REVERT: B 187 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: C 11 VAL cc_start: 0.9049 (p) cc_final: 0.8824 (m) REVERT: C 75 GLU cc_start: 0.7247 (tt0) cc_final: 0.7009 (tt0) REVERT: C 140 LYS cc_start: 0.8347 (mttt) cc_final: 0.8073 (mtpp) REVERT: D 39 MET cc_start: 0.7904 (tpt) cc_final: 0.7321 (tpt) REVERT: D 54 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7809 (m) REVERT: E 103 ASP cc_start: 0.7578 (m-30) cc_final: 0.7334 (m-30) REVERT: E 180 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6671 (mm-30) REVERT: E 215 MET cc_start: 0.8111 (mtp) cc_final: 0.7577 (mtp) outliers start: 15 outliers final: 13 residues processed: 170 average time/residue: 0.2525 time to fit residues: 58.7470 Evaluate side-chains 174 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 54 THR 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 D residue 216 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.0020 chunk 107 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 125 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3215 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= 0.177 Angle : 0.484 7.854 14421 Z= 0.242 Chirality : 0.040 0.158 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.600 17.389 1421 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.36 % Allowed : 8.97 % Favored : 89.67 % 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: 2.10 (0.23), residues: 1319 helix: 1.71 (0.18), residues: 892 sheet: -1.08 (0.66), residues: 45 loop : 1.20 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 80 HIS 0.005 0.000 HIS A 120 PHE 0.012 0.001 PHE E 32 TYR 0.012 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 178 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 1.196 Fit side-chains REVERT: B 39 MET cc_start: 0.8381 (tpt) cc_final: 0.7907 (tpt) REVERT: B 76 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7591 (mm-30) REVERT: C 11 VAL cc_start: 0.9035 (p) cc_final: 0.8827 (m) REVERT: C 140 LYS cc_start: 0.8314 (mttt) cc_final: 0.8073 (mtpp) REVERT: D 39 MET cc_start: 0.7881 (tpt) cc_final: 0.7320 (tpt) REVERT: D 54 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7788 (m) REVERT: E 103 ASP cc_start: 0.7571 (m-30) cc_final: 0.7309 (m-30) REVERT: E 113 GLU cc_start: 0.8247 (mp0) cc_final: 0.7973 (mp0) REVERT: E 180 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6633 (mm-30) REVERT: E 215 MET cc_start: 0.8056 (mtp) cc_final: 0.7747 (mtp) outliers start: 15 outliers final: 11 residues processed: 171 average time/residue: 0.2413 time to fit residues: 56.8392 Evaluate side-chains 168 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 54 THR 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 D residue 216 THR Chi-restraints excluded: chain E residue 144 MET 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: 0.6980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 121 optimal weight: 0.1980 chunk 104 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 64 optimal weight: 0.0170 chunk 83 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** C 179 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: 0.7332 moved from start: 0.3352 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 : 0.500 8.487 14421 Z= 0.248 Chirality : 0.040 0.161 1639 Planarity : 0.004 0.037 1867 Dihedral : 3.535 16.495 1421 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.18 % Allowed : 9.24 % Favored : 89.58 % 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: 2.13 (0.23), residues: 1319 helix: 1.75 (0.18), residues: 895 sheet: -1.01 (0.66), residues: 45 loop : 1.18 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 80 HIS 0.006 0.000 HIS A 120 PHE 0.015 0.001 PHE F 32 TYR 0.013 0.001 TYR F 169 ARG 0.002 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 171 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 1.232 Fit side-chains REVERT: A 167 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7864 (mtp180) REVERT: B 39 MET cc_start: 0.8353 (tpt) cc_final: 0.7882 (tpt) REVERT: B 76 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7632 (mm-30) REVERT: C 11 VAL cc_start: 0.9021 (p) cc_final: 0.8821 (m) REVERT: C 140 LYS cc_start: 0.8272 (mttt) cc_final: 0.8071 (mtpp) REVERT: D 39 MET cc_start: 0.7867 (tpt) cc_final: 0.7292 (tpt) REVERT: D 54 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7771 (m) REVERT: E 103 ASP cc_start: 0.7584 (m-30) cc_final: 0.7322 (m-30) REVERT: E 180 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6638 (mm-30) REVERT: E 215 MET cc_start: 0.8034 (mtp) cc_final: 0.7539 (mtp) outliers start: 13 outliers final: 11 residues processed: 166 average time/residue: 0.2431 time to fit residues: 55.8376 Evaluate side-chains 161 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 54 THR 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 D residue 216 THR Chi-restraints excluded: chain E residue 144 MET 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: 5.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 107 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 75 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.179803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.153021 restraints weight = 10844.814| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.86 r_work: 0.3501 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3371 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= 0.181 Angle : 0.511 8.409 14421 Z= 0.251 Chirality : 0.040 0.155 1639 Planarity : 0.004 0.037 1867 Dihedral : 3.549 16.548 1421 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.09 % Allowed : 10.05 % Favored : 88.86 % 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: 2.13 (0.23), residues: 1319 helix: 1.75 (0.18), residues: 895 sheet: -0.96 (0.66), residues: 45 loop : 1.16 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.006 0.000 HIS A 120 PHE 0.012 0.001 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.006 0.000 ARG F 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.96 seconds wall clock time: 43 minutes 1.56 seconds (2581.56 seconds total)