Starting phenix.real_space_refine on Sat Dec 28 20:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f02_31394/12_2024/7f02_31394.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f02_31394/12_2024/7f02_31394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f02_31394/12_2024/7f02_31394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f02_31394/12_2024/7f02_31394.map" model { file = "/net/cci-nas-00/data/ceres_data/7f02_31394/12_2024/7f02_31394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f02_31394/12_2024/7f02_31394.cif" } resolution = 3.24 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= 0.002 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5778 2.51 5 N 1505 2.21 5 O 1501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8835 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1848 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "F" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.39, per 1000 atoms: 0.72 Number of scatterers: 8835 At special positions: 0 Unit cell: (98.176, 99.008, 118.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 3 15.00 Mg 2 11.99 O 1501 8.00 N 1505 7.00 C 5778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 64.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.582A pdb=" N LEU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.873A pdb=" N GLY A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.569A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 removed outlier: 3.609A pdb=" N GLN A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 173 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 176 " --> pdb=" O HIS A 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.775A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 88 through 105 removed outlier: 3.542A pdb=" N ALA B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B 102 " --> pdb=" O MET B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 Proline residue: B 113 - end of helix removed outlier: 3.802A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.764A pdb=" N VAL B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 133 " --> pdb=" O MET B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 154 removed outlier: 3.687A pdb=" N GLY B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Proline residue: B 146 - end of helix removed outlier: 3.535A pdb=" N LEU B 150 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 165 removed outlier: 3.904A pdb=" N ILE B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 164 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 165 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 180 removed outlier: 3.505A pdb=" N ALA B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 190 through 204 removed outlier: 4.437A pdb=" N LEU B 196 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 220 Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 20 through 28 removed outlier: 4.615A pdb=" N TRP C 24 " --> pdb=" O TRP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.509A pdb=" N TRP C 66 " --> pdb=" O PRO C 62 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.915A pdb=" N VAL C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 96 removed outlier: 3.673A pdb=" N ALA C 92 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 120 Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 126 through 147 removed outlier: 4.113A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 185 Proline residue: C 171 - end of helix removed outlier: 3.644A pdb=" N TRP C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 199 through 226 removed outlier: 3.724A pdb=" N LEU C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.210A pdb=" N GLU C 237 " --> pdb=" O TRP C 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 54 Proline residue: D 31 - end of helix removed outlier: 4.222A pdb=" N LEU D 47 " --> pdb=" O HIS D 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 49 Processing helix chain 'E' and resid 90 through 98 removed outlier: 3.570A pdb=" N ASN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR E 98 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 128 through 138 removed outlier: 4.001A pdb=" N ARG E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG E 134 " --> pdb=" O GLY E 130 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 142 Processing helix chain 'E' and resid 161 through 176 removed outlier: 3.774A pdb=" N GLN E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY E 176 " --> pdb=" O HIS E 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 17 removed outlier: 3.588A pdb=" N ARG F 16 " --> pdb=" O ARG F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 39 removed outlier: 3.833A pdb=" N PHE F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Proline residue: F 36 - end of helix Processing helix chain 'F' and resid 42 through 66 Proline residue: F 51 - end of helix removed outlier: 3.710A pdb=" N TRP F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 69 No H-bonds generated for 'chain 'F' and resid 67 through 69' Processing helix chain 'F' and resid 70 through 75 removed outlier: 4.120A pdb=" N GLN F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 104 Processing helix chain 'F' and resid 104 through 111 removed outlier: 3.801A pdb=" N LEU F 111 " --> pdb=" O PRO F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 120 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 136 through 152 Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 158 through 166 Processing helix chain 'F' and resid 169 through 182 Processing helix chain 'F' and resid 190 through 205 removed outlier: 3.584A pdb=" N ILE F 195 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU F 196 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 199 " --> pdb=" O ILE F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 220 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 4.085A pdb=" N PHE A 17 " --> pdb=" O CYS A 9 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU A 7 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 57 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A 7 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA A 55 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.390A pdb=" N LEU A 77 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP A 29 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE A 197 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN A 31 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA4, first strand: chain 'E' and resid 15 through 20 removed outlier: 6.023A pdb=" N SER E 18 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N CYS E 9 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU E 7 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA E 55 " --> pdb=" O LEU E 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 79 removed outlier: 6.143A pdb=" N LEU E 77 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU E 28 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU E 181 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL E 30 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TRP E 29 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE E 197 " --> pdb=" O TRP E 29 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN E 31 " --> pdb=" O ILE E 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 59 through 60 438 hydrogen bonds defined for protein. 1272 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: 2.51 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1353 1.31 - 1.43: 2403 1.43 - 1.56: 5199 1.56 - 1.69: 2 1.69 - 1.81: 87 Bond restraints: 9044 Sorted by residual: bond pdb=" C11 3PE C 302 " pdb=" O13 3PE C 302 " ideal model delta sigma weight residual 1.408 1.486 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O3 PO4 E 301 " pdb=" P PO4 E 301 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.86e+00 bond pdb=" O3 PO4 A 301 " pdb=" P PO4 A 301 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O4 PO4 A 301 " pdb=" P PO4 A 301 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 8.87e+00 bond pdb=" O2 PO4 E 301 " pdb=" P PO4 E 301 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.65e+00 ... (remaining 9039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 12109 2.25 - 4.50: 187 4.50 - 6.75: 33 6.75 - 9.00: 1 9.00 - 11.25: 2 Bond angle restraints: 12332 Sorted by residual: angle pdb=" N VAL C 35 " pdb=" CA VAL C 35 " pdb=" C VAL C 35 " ideal model delta sigma weight residual 113.53 106.37 7.16 9.80e-01 1.04e+00 5.34e+01 angle pdb=" N ILE C 56 " pdb=" CA ILE C 56 " pdb=" C ILE C 56 " ideal model delta sigma weight residual 112.98 107.81 5.17 1.25e+00 6.40e-01 1.71e+01 angle pdb=" C12 3PE C 302 " pdb=" C11 3PE C 302 " pdb=" O13 3PE C 302 " ideal model delta sigma weight residual 108.28 119.53 -11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" N ILE C 194 " pdb=" CA ILE C 194 " pdb=" C ILE C 194 " ideal model delta sigma weight residual 113.71 110.29 3.42 9.50e-01 1.11e+00 1.30e+01 angle pdb=" N TYR C 54 " pdb=" CA TYR C 54 " pdb=" C TYR C 54 " ideal model delta sigma weight residual 111.81 107.00 4.81 1.44e+00 4.82e-01 1.12e+01 ... (remaining 12327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4772 17.86 - 35.73: 432 35.73 - 53.59: 86 53.59 - 71.46: 15 71.46 - 89.32: 6 Dihedral angle restraints: 5311 sinusoidal: 2087 harmonic: 3224 Sorted by residual: dihedral pdb=" CA TRP C 39 " pdb=" C TRP C 39 " pdb=" N GLY C 40 " pdb=" CA GLY C 40 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA THR E 166 " pdb=" C THR E 166 " pdb=" N GLN E 167 " pdb=" CA GLN E 167 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA LEU B 131 " pdb=" C LEU B 131 " pdb=" N THR B 132 " pdb=" CA THR B 132 " ideal model delta harmonic sigma weight residual 180.00 159.01 20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1035 0.041 - 0.081: 314 0.081 - 0.122: 95 0.122 - 0.163: 9 0.163 - 0.203: 2 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CB THR A 182 " pdb=" CA THR A 182 " pdb=" OG1 THR A 182 " pdb=" CG2 THR A 182 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB THR E 182 " pdb=" CA THR E 182 " pdb=" OG1 THR E 182 " pdb=" CG2 THR E 182 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CA ILE A 180 " pdb=" N ILE A 180 " pdb=" C ILE A 180 " pdb=" CB ILE A 180 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 1452 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 123 " -0.017 2.00e-02 2.50e+03 1.28e-02 4.10e+00 pdb=" CG TRP C 123 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP C 123 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 123 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 123 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 123 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 123 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 123 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 123 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 123 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 89 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO F 90 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 90 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 90 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 22 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO C 23 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 23 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 23 " -0.025 5.00e-02 4.00e+02 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 30 2.50 - 3.10: 6256 3.10 - 3.70: 13110 3.70 - 4.30: 18975 4.30 - 4.90: 32331 Nonbonded interactions: 70702 Sorted by model distance: nonbonded pdb=" NE2 HIS E 81 " pdb="MG MG E 300 " model vdw 1.895 2.250 nonbonded pdb=" NE2 HIS A 81 " pdb="MG MG A 300 " model vdw 1.895 2.250 nonbonded pdb="MG MG A 300 " pdb=" O1 PO4 A 301 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR E 41 " pdb="MG MG E 300 " model vdw 2.061 2.170 nonbonded pdb=" OG1 THR A 41 " pdb="MG MG A 300 " model vdw 2.062 2.170 ... (remaining 70697 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 23.830 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.004 0.078 9044 Z= 0.279 Angle : 0.693 11.254 12332 Z= 0.366 Chirality : 0.042 0.203 1455 Planarity : 0.005 0.046 1521 Dihedral : 14.417 89.323 3227 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.68 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.26), residues: 1118 helix: -0.16 (0.21), residues: 677 sheet: -0.94 (0.75), residues: 58 loop : -2.15 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 123 HIS 0.006 0.001 HIS E 96 PHE 0.021 0.001 PHE A 97 TYR 0.006 0.001 TYR F 124 ARG 0.007 0.000 ARG F 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 HIS cc_start: 0.8110 (t70) cc_final: 0.7732 (t70) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2372 time to fit residues: 69.2457 Evaluate side-chains 190 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN E 184 HIS ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9044 Z= 0.308 Angle : 0.694 6.964 12332 Z= 0.350 Chirality : 0.044 0.147 1455 Planarity : 0.005 0.049 1521 Dihedral : 7.378 71.261 1247 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.23 % Favored : 91.68 % Rotamer: Outliers : 2.29 % Allowed : 10.91 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.26), residues: 1118 helix: 0.05 (0.21), residues: 692 sheet: -1.16 (0.75), residues: 58 loop : -2.30 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 123 HIS 0.010 0.001 HIS A 73 PHE 0.013 0.002 PHE C 41 TYR 0.016 0.002 TYR F 124 ARG 0.004 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: F 100 HIS cc_start: 0.8389 (t70) cc_final: 0.7676 (t70) outliers start: 21 outliers final: 12 residues processed: 199 average time/residue: 0.2316 time to fit residues: 61.9830 Evaluate side-chains 194 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 76 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9044 Z= 0.187 Angle : 0.628 13.289 12332 Z= 0.309 Chirality : 0.042 0.151 1455 Planarity : 0.005 0.049 1521 Dihedral : 7.068 69.957 1247 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.16 % Favored : 92.75 % Rotamer: Outliers : 1.64 % Allowed : 15.16 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.27), residues: 1118 helix: 0.37 (0.22), residues: 683 sheet: -1.19 (0.74), residues: 58 loop : -2.21 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 123 HIS 0.007 0.001 HIS A 73 PHE 0.012 0.001 PHE A 97 TYR 0.007 0.001 TYR F 124 ARG 0.009 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7665 (tp30) cc_final: 0.7197 (tp30) REVERT: F 100 HIS cc_start: 0.8308 (t70) cc_final: 0.7784 (t70) outliers start: 15 outliers final: 9 residues processed: 195 average time/residue: 0.2395 time to fit residues: 62.8936 Evaluate side-chains 191 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0670 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.0770 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 overall best weight: 0.8878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9044 Z= 0.200 Angle : 0.615 9.030 12332 Z= 0.303 Chirality : 0.042 0.145 1455 Planarity : 0.005 0.051 1521 Dihedral : 6.683 67.815 1247 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.60 % Favored : 92.31 % Rotamer: Outliers : 2.62 % Allowed : 15.92 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.27), residues: 1118 helix: 0.48 (0.22), residues: 684 sheet: -1.13 (0.74), residues: 58 loop : -2.18 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 39 HIS 0.006 0.001 HIS A 73 PHE 0.012 0.001 PHE B 3 TYR 0.009 0.001 TYR F 124 ARG 0.009 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7543 (mtm-85) REVERT: B 133 LEU cc_start: 0.8248 (tp) cc_final: 0.7892 (tp) REVERT: F 10 GLU cc_start: 0.7700 (tp30) cc_final: 0.7274 (tp30) REVERT: F 100 HIS cc_start: 0.8296 (t70) cc_final: 0.7783 (t70) outliers start: 24 outliers final: 13 residues processed: 200 average time/residue: 0.2350 time to fit residues: 63.4722 Evaluate side-chains 200 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.0470 chunk 1 optimal weight: 0.0270 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9044 Z= 0.209 Angle : 0.614 9.315 12332 Z= 0.305 Chirality : 0.042 0.140 1455 Planarity : 0.005 0.051 1521 Dihedral : 6.542 67.060 1247 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.42 % Favored : 92.49 % Rotamer: Outliers : 2.18 % Allowed : 17.88 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.27), residues: 1118 helix: 0.52 (0.22), residues: 688 sheet: -1.01 (0.74), residues: 58 loop : -2.20 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 123 HIS 0.006 0.001 HIS A 73 PHE 0.011 0.001 PHE B 3 TYR 0.010 0.001 TYR F 124 ARG 0.007 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: B 2 MET cc_start: 0.6085 (tpt) cc_final: 0.5848 (ttm) REVERT: B 174 ILE cc_start: 0.8032 (mt) cc_final: 0.7770 (mt) REVERT: C 54 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.5935 (t80) REVERT: C 57 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7678 (mt) REVERT: F 10 GLU cc_start: 0.7653 (tp30) cc_final: 0.7262 (tp30) REVERT: F 100 HIS cc_start: 0.8317 (t70) cc_final: 0.7776 (t70) outliers start: 20 outliers final: 16 residues processed: 203 average time/residue: 0.2326 time to fit residues: 63.6164 Evaluate side-chains 206 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9044 Z= 0.322 Angle : 0.672 9.632 12332 Z= 0.335 Chirality : 0.045 0.152 1455 Planarity : 0.005 0.050 1521 Dihedral : 6.673 68.000 1247 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.59 % Favored : 91.32 % Rotamer: Outliers : 3.16 % Allowed : 18.21 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.26), residues: 1118 helix: 0.42 (0.21), residues: 683 sheet: -1.07 (0.74), residues: 58 loop : -2.25 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 39 HIS 0.006 0.001 HIS A 73 PHE 0.011 0.001 PHE D 19 TYR 0.015 0.001 TYR F 124 ARG 0.012 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 68 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7331 (mtm-85) REVERT: B 174 ILE cc_start: 0.8087 (mt) cc_final: 0.7824 (mt) REVERT: F 10 GLU cc_start: 0.7728 (tp30) cc_final: 0.7382 (tp30) REVERT: F 100 HIS cc_start: 0.8359 (t70) cc_final: 0.7902 (t70) outliers start: 29 outliers final: 19 residues processed: 207 average time/residue: 0.2291 time to fit residues: 63.7513 Evaluate side-chains 207 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 49 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9044 Z= 0.192 Angle : 0.631 9.817 12332 Z= 0.308 Chirality : 0.042 0.147 1455 Planarity : 0.005 0.053 1521 Dihedral : 6.502 68.685 1247 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.16 % Favored : 92.75 % Rotamer: Outliers : 2.51 % Allowed : 20.17 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.27), residues: 1118 helix: 0.68 (0.22), residues: 679 sheet: -0.88 (0.74), residues: 58 loop : -2.20 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 123 HIS 0.006 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.007 0.001 TYR F 124 ARG 0.010 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7470 (mt-10) REVERT: B 108 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8612 (mt) REVERT: B 133 LEU cc_start: 0.8243 (tp) cc_final: 0.7993 (tp) REVERT: B 174 ILE cc_start: 0.8042 (mt) cc_final: 0.7781 (mt) REVERT: E 182 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8016 (p) REVERT: F 10 GLU cc_start: 0.7629 (tp30) cc_final: 0.7365 (tp30) REVERT: F 100 HIS cc_start: 0.8307 (t70) cc_final: 0.7820 (t70) REVERT: F 101 TRP cc_start: 0.8746 (t60) cc_final: 0.8501 (t60) outliers start: 23 outliers final: 16 residues processed: 200 average time/residue: 0.2458 time to fit residues: 65.6659 Evaluate side-chains 202 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN E 171 GLN F 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9044 Z= 0.198 Angle : 0.648 10.511 12332 Z= 0.312 Chirality : 0.042 0.158 1455 Planarity : 0.005 0.053 1521 Dihedral : 6.394 70.032 1247 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.42 % Favored : 92.49 % Rotamer: Outliers : 3.16 % Allowed : 20.72 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.27), residues: 1118 helix: 0.69 (0.21), residues: 688 sheet: -0.75 (0.76), residues: 58 loop : -2.18 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 55 HIS 0.007 0.001 HIS D 38 PHE 0.012 0.001 PHE B 3 TYR 0.012 0.001 TYR C 54 ARG 0.009 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8631 (mt) REVERT: B 133 LEU cc_start: 0.8104 (tp) cc_final: 0.7889 (tp) REVERT: E 182 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7947 (p) REVERT: F 10 GLU cc_start: 0.7651 (tp30) cc_final: 0.7399 (tp30) REVERT: F 100 HIS cc_start: 0.8307 (t70) cc_final: 0.7819 (t70) outliers start: 29 outliers final: 21 residues processed: 206 average time/residue: 0.2378 time to fit residues: 65.1484 Evaluate side-chains 210 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 HIS Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9044 Z= 0.237 Angle : 0.666 9.639 12332 Z= 0.325 Chirality : 0.043 0.166 1455 Planarity : 0.005 0.054 1521 Dihedral : 6.410 70.651 1247 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.69 % Favored : 92.22 % Rotamer: Outliers : 3.05 % Allowed : 20.50 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.27), residues: 1118 helix: 0.71 (0.21), residues: 685 sheet: -0.75 (0.75), residues: 58 loop : -2.21 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 123 HIS 0.008 0.001 HIS D 38 PHE 0.012 0.001 PHE B 3 TYR 0.011 0.001 TYR C 54 ARG 0.009 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8632 (mt) REVERT: B 133 LEU cc_start: 0.8112 (tp) cc_final: 0.7910 (tp) REVERT: B 174 ILE cc_start: 0.8048 (mt) cc_final: 0.7802 (mt) REVERT: E 182 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.7917 (p) REVERT: F 10 GLU cc_start: 0.7670 (tp30) cc_final: 0.7431 (tp30) REVERT: F 100 HIS cc_start: 0.8344 (t70) cc_final: 0.7920 (t70) outliers start: 28 outliers final: 22 residues processed: 202 average time/residue: 0.2440 time to fit residues: 66.1907 Evaluate side-chains 209 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 HIS Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN E 171 GLN F 17 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9044 Z= 0.215 Angle : 0.664 9.608 12332 Z= 0.322 Chirality : 0.043 0.159 1455 Planarity : 0.005 0.054 1521 Dihedral : 6.348 71.719 1247 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.69 % Favored : 92.22 % Rotamer: Outliers : 2.51 % Allowed : 20.94 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.27), residues: 1118 helix: 0.74 (0.21), residues: 685 sheet: -0.77 (0.74), residues: 58 loop : -2.20 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 55 HIS 0.009 0.001 HIS D 38 PHE 0.013 0.001 PHE B 3 TYR 0.010 0.001 TYR C 54 ARG 0.008 0.000 ARG B 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8620 (mt) REVERT: E 182 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.7916 (p) REVERT: F 10 GLU cc_start: 0.7672 (tp30) cc_final: 0.7448 (tp30) REVERT: F 100 HIS cc_start: 0.8331 (t70) cc_final: 0.7909 (t70) outliers start: 23 outliers final: 21 residues processed: 195 average time/residue: 0.2400 time to fit residues: 62.2799 Evaluate side-chains 209 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 HIS Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108645 restraints weight = 14107.780| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.23 r_work: 0.3329 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9044 Z= 0.200 Angle : 0.662 9.776 12332 Z= 0.320 Chirality : 0.043 0.161 1455 Planarity : 0.004 0.054 1521 Dihedral : 6.282 72.174 1247 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer: Outliers : 2.84 % Allowed : 20.50 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.27), residues: 1118 helix: 0.79 (0.21), residues: 685 sheet: -0.81 (0.74), residues: 58 loop : -2.17 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 123 HIS 0.009 0.001 HIS D 38 PHE 0.012 0.001 PHE B 3 TYR 0.010 0.001 TYR C 54 ARG 0.008 0.000 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2240.31 seconds wall clock time: 41 minutes 49.56 seconds (2509.56 seconds total)