Starting phenix.real_space_refine on Thu Mar 13 09:27:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vfj_31956/03_2025/7vfj_31956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vfj_31956/03_2025/7vfj_31956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vfj_31956/03_2025/7vfj_31956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vfj_31956/03_2025/7vfj_31956.map" model { file = "/net/cci-nas-00/data/ceres_data/7vfj_31956/03_2025/7vfj_31956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vfj_31956/03_2025/7vfj_31956.cif" } resolution = 3.98 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= 0.032 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5745 2.51 5 N 1504 2.21 5 O 1485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8780 Number of models: 1 Model: "" Number of chains: 6 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} Time building chain proxies: 5.94, per 1000 atoms: 0.68 Number of scatterers: 8780 At special positions: 0 Unit cell: (102.336, 99.84, 114.816, 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 46 16.00 O 1485 8.00 N 1504 7.00 C 5745 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: 2.42 Conformation dependent library (CDL) restraints added in 1.0 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: 49 helices and 6 sheets defined 65.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.668A pdb=" N LEU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.561A pdb=" N ASN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.708A pdb=" N GLU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.574A pdb=" N GLN A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.793A pdb=" N GLN A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 4.063A pdb=" N GLN A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 176 " --> pdb=" O HIS A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 176' Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.844A pdb=" N LYS A 193 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.585A pdb=" N ILE B 6 " --> pdb=" O MET B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.785A pdb=" N LEU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 42 through 75 removed outlier: 3.838A pdb=" N LEU B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 3.747A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 88 through 120 removed outlier: 3.663A pdb=" N ALA B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Proline residue: B 113 - end of helix removed outlier: 3.531A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.525A pdb=" N VAL B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 149 Proline residue: B 146 - end of helix removed outlier: 4.322A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.765A pdb=" N SER B 162 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 185 removed outlier: 3.807A pdb=" N LEU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Proline residue: B 171 - end of helix removed outlier: 4.103A pdb=" N PHE B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 4.197A pdb=" N LEU B 196 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 3.625A 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 21 through 32 removed outlier: 3.544A pdb=" N ALA C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 31 " --> pdb=" O ILE C 27 " (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 80 removed outlier: 3.728A pdb=" N SER C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 75 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 96 removed outlier: 3.659A pdb=" N ALA C 92 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 120 removed outlier: 3.523A pdb=" N LYS C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 126 through 147 removed outlier: 4.589A 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: 3.830A pdb=" N TRP C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 229 removed outlier: 3.979A pdb=" N LEU C 202 " --> pdb=" O MET C 198 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.186A 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: 3.522A pdb=" N LEU D 47 " --> pdb=" O HIS D 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 49 Processing helix chain 'E' and resid 70 through 75 removed outlier: 3.734A pdb=" N GLN E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 75' Processing helix chain 'E' and resid 90 through 98 removed outlier: 3.942A pdb=" N TYR E 98 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 128 through 138 removed outlier: 3.953A pdb=" N ARG E 134 " --> pdb=" O GLY E 130 " (cutoff:3.500A) removed outlier: 3.534A 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 158 through 176 removed outlier: 4.116A pdb=" N ASP E 163 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 16 removed outlier: 3.774A pdb=" N ARG F 16 " --> pdb=" O ARG F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 40 Proline residue: F 36 - end of helix Processing helix chain 'F' and resid 42 through 67 Proline residue: F 51 - end of helix removed outlier: 3.516A pdb=" N TRP F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 111 removed outlier: 4.038A pdb=" N LEU F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Proline residue: F 107 - end of helix removed outlier: 3.868A 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 152 Proline residue: F 138 - end of helix Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 158 through 166 Processing helix chain 'F' and resid 169 through 185 removed outlier: 4.437A pdb=" N MET F 185 " --> pdb=" O ASP F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 220 removed outlier: 3.525A pdb=" N ILE F 195 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) Proline residue: F 208 - end of helix removed outlier: 3.607A pdb=" N GLN F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.004A pdb=" N SER A 18 " --> pdb=" O CYS A 9 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N CYS A 9 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU A 7 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 6.146A 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: 6.358A pdb=" N LEU A 77 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP A 151 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 79 " --> pdb=" O ASP A 151 " (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: 6.213A pdb=" N SER E 18 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N CYS E 9 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU E 6 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU E 57 " --> pdb=" O GLU E 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 79 removed outlier: 5.953A pdb=" N LEU E 77 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP E 29 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE E 197 " --> pdb=" O TRP E 29 " (cutoff:3.500A) removed outlier: 6.300A 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 60 456 hydrogen bonds defined for protein. 1332 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: 2.60 Time building geometry restraints manager: 2.85 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: 2784 1.34 - 1.46: 1833 1.46 - 1.58: 4289 1.58 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 8994 Sorted by residual: bond pdb=" CB PRO E 186 " pdb=" CG PRO E 186 " ideal model delta sigma weight residual 1.492 1.670 -0.178 5.00e-02 4.00e+02 1.26e+01 bond pdb=" CG PRO E 186 " pdb=" CD PRO E 186 " ideal model delta sigma weight residual 1.503 1.422 0.081 3.40e-02 8.65e+02 5.67e+00 bond pdb=" C ASN B 23 " pdb=" N PRO B 24 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.63e+00 bond pdb=" N PRO E 186 " pdb=" CD PRO E 186 " ideal model delta sigma weight residual 1.473 1.498 -0.025 1.40e-02 5.10e+03 3.08e+00 bond pdb=" CG LEU E 50 " pdb=" CD1 LEU E 50 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 ... (remaining 8989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 12132 3.19 - 6.38: 131 6.38 - 9.57: 7 9.57 - 12.77: 2 12.77 - 15.96: 1 Bond angle restraints: 12273 Sorted by residual: angle pdb=" CA PRO E 186 " pdb=" N PRO E 186 " pdb=" CD PRO E 186 " ideal model delta sigma weight residual 112.00 96.04 15.96 1.40e+00 5.10e-01 1.30e+02 angle pdb=" N PRO E 186 " pdb=" CD PRO E 186 " pdb=" CG PRO E 186 " ideal model delta sigma weight residual 103.20 94.96 8.24 1.50e+00 4.44e-01 3.02e+01 angle pdb=" C ASP A 12 " pdb=" CA ASP A 12 " pdb=" CB ASP A 12 " ideal model delta sigma weight residual 117.23 110.44 6.79 1.36e+00 5.41e-01 2.49e+01 angle pdb=" CA MET F 129 " pdb=" CB MET F 129 " pdb=" CG MET F 129 " ideal model delta sigma weight residual 114.10 122.00 -7.90 2.00e+00 2.50e-01 1.56e+01 angle pdb=" N MET F 129 " pdb=" CA MET F 129 " pdb=" CB MET F 129 " ideal model delta sigma weight residual 110.30 116.05 -5.75 1.54e+00 4.22e-01 1.39e+01 ... (remaining 12268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4763 17.43 - 34.86: 434 34.86 - 52.29: 62 52.29 - 69.72: 7 69.72 - 87.15: 4 Dihedral angle restraints: 5270 sinusoidal: 2046 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 180.00 153.96 26.04 0 5.00e+00 4.00e-02 2.71e+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 180.00 156.12 23.88 0 5.00e+00 4.00e-02 2.28e+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 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 5267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1187 0.057 - 0.114: 242 0.114 - 0.171: 22 0.171 - 0.228: 2 0.228 - 0.285: 1 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CB ILE B 163 " pdb=" CA ILE B 163 " pdb=" CG1 ILE B 163 " pdb=" CG2 ILE B 163 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA PRO E 186 " pdb=" N PRO E 186 " pdb=" C PRO E 186 " pdb=" CB PRO E 186 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+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 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1451 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 185 " 0.081 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO E 186 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO E 186 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 186 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 29 " -0.020 2.00e-02 2.50e+03 1.82e-02 8.24e+00 pdb=" CG TRP A 29 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 29 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 29 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 29 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 29 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 29 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 29 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 141 " 0.010 2.00e-02 2.50e+03 1.63e-02 6.67e+00 pdb=" CG TRP E 141 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP E 141 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP E 141 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 141 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 141 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 141 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 141 " 0.001 2.00e-02 2.50e+03 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 171 2.69 - 3.24: 9180 3.24 - 3.79: 13914 3.79 - 4.35: 17839 4.35 - 4.90: 28499 Nonbonded interactions: 69603 Sorted by model distance: nonbonded pdb=" OD1 ASP B 122 " pdb=" N VAL B 123 " model vdw 2.134 3.120 nonbonded pdb=" OG1 THR A 90 " pdb=" OE1 GLU A 93 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR A 146 " pdb=" O GLY A 176 " model vdw 2.192 3.040 nonbonded pdb=" O VAL F 159 " pdb=" OG SER F 162 " model vdw 2.222 3.040 nonbonded pdb=" NE2 HIS E 99 " pdb=" O ASP E 101 " model vdw 2.239 3.120 ... (remaining 69598 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 group one per residue 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: 2.210 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.660 Find NCS groups from input model: 0.260 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:4.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 0.178 8994 Z= 0.228 Angle : 0.833 15.957 12273 Z= 0.451 Chirality : 0.045 0.285 1454 Planarity : 0.005 0.110 1519 Dihedral : 13.075 87.155 3186 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.98 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.92 (0.26), residues: 1118 helix: 0.37 (0.22), residues: 649 sheet: -1.22 (0.68), residues: 58 loop : -2.09 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 29 HIS 0.018 0.001 HIS A 96 PHE 0.026 0.002 PHE B 142 TYR 0.029 0.002 TYR C 139 ARG 0.004 0.000 ARG B 68 *********************** 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 325 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.6921 (t0) cc_final: 0.6446 (t0) REVERT: B 122 ASP cc_start: 0.8236 (t0) cc_final: 0.7935 (t0) REVERT: B 135 LEU cc_start: 0.9039 (mt) cc_final: 0.8446 (tp) REVERT: B 177 THR cc_start: 0.8289 (p) cc_final: 0.8034 (p) REVERT: B 185 MET cc_start: 0.8138 (ppp) cc_final: 0.7791 (ppp) REVERT: D 1 MET cc_start: -0.0994 (tpt) cc_final: -0.3193 (pmm) REVERT: F 7 PHE cc_start: 0.8585 (t80) cc_final: 0.7826 (t80) REVERT: F 11 LEU cc_start: 0.9158 (mt) cc_final: 0.8759 (mt) REVERT: F 17 HIS cc_start: 0.7772 (t-90) cc_final: 0.7524 (t-90) REVERT: F 181 ASP cc_start: 0.8554 (m-30) cc_final: 0.8004 (t0) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1728 time to fit residues: 80.2080 Evaluate side-chains 267 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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: 5.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.088607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.073238 restraints weight = 35040.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.075269 restraints weight = 19967.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.076677 restraints weight = 13663.883| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8994 Z= 0.244 Angle : 0.764 9.052 12273 Z= 0.375 Chirality : 0.046 0.299 1454 Planarity : 0.005 0.051 1519 Dihedral : 4.924 28.188 1206 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.59 % Favored : 91.14 % Rotamer: Outliers : 2.51 % Allowed : 16.03 % 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: -0.97 (0.26), residues: 1118 helix: 0.31 (0.21), residues: 674 sheet: -0.84 (0.75), residues: 52 loop : -2.29 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 29 HIS 0.005 0.001 HIS E 99 PHE 0.027 0.002 PHE A 97 TYR 0.019 0.002 TYR C 139 ARG 0.011 0.001 ARG F 156 *********************** 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 305 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8718 (tp) cc_final: 0.8437 (mp) REVERT: A 169 MET cc_start: 0.7542 (tpt) cc_final: 0.7259 (tpp) REVERT: B 104 THR cc_start: 0.9182 (p) cc_final: 0.8972 (t) REVERT: B 122 ASP cc_start: 0.8166 (t0) cc_final: 0.7918 (t0) REVERT: B 135 LEU cc_start: 0.9084 (mt) cc_final: 0.8526 (tt) REVERT: C 70 ILE cc_start: 0.9345 (tp) cc_final: 0.9105 (tp) REVERT: C 74 MET cc_start: 0.8606 (mmm) cc_final: 0.8403 (mtt) REVERT: C 139 TYR cc_start: 0.8619 (m-10) cc_final: 0.8381 (m-10) REVERT: D 1 MET cc_start: -0.0860 (tpt) cc_final: -0.3107 (pmm) REVERT: D 41 MET cc_start: 0.8521 (ppp) cc_final: 0.8281 (ppp) REVERT: E 121 ASP cc_start: 0.8457 (t0) cc_final: 0.8145 (t0) REVERT: F 83 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8103 (pmm) REVERT: F 181 ASP cc_start: 0.8579 (m-30) cc_final: 0.7899 (t0) REVERT: F 192 TYR cc_start: 0.8580 (m-80) cc_final: 0.8031 (m-80) outliers start: 23 outliers final: 17 residues processed: 292 average time/residue: 0.1690 time to fit residues: 71.1306 Evaluate side-chains 280 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 262 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.088279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.072846 restraints weight = 35957.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.074901 restraints weight = 20462.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.076298 restraints weight = 13990.794| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8994 Z= 0.211 Angle : 0.732 11.234 12273 Z= 0.353 Chirality : 0.046 0.296 1454 Planarity : 0.004 0.052 1519 Dihedral : 4.855 25.031 1206 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.60 % Favored : 92.13 % Rotamer: Outliers : 4.58 % Allowed : 18.87 % 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: -0.82 (0.26), residues: 1118 helix: 0.42 (0.20), residues: 682 sheet: -0.76 (0.77), residues: 52 loop : -2.25 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 29 HIS 0.003 0.001 HIS A 81 PHE 0.022 0.002 PHE A 97 TYR 0.015 0.001 TYR C 15 ARG 0.004 0.000 ARG F 216 *********************** 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 334 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8744 (tp) cc_final: 0.8492 (mp) REVERT: B 100 HIS cc_start: 0.8385 (t70) cc_final: 0.8011 (t70) REVERT: B 135 LEU cc_start: 0.9151 (mt) cc_final: 0.8636 (tt) REVERT: B 177 THR cc_start: 0.7926 (p) cc_final: 0.7561 (t) REVERT: B 185 MET cc_start: 0.8112 (ppp) cc_final: 0.7797 (ppp) REVERT: C 54 TYR cc_start: 0.7695 (t80) cc_final: 0.7234 (t80) REVERT: C 70 ILE cc_start: 0.9332 (tp) cc_final: 0.9018 (tp) REVERT: D 1 MET cc_start: -0.0482 (tpt) cc_final: -0.2651 (pmm) REVERT: D 41 MET cc_start: 0.8508 (ppp) cc_final: 0.8232 (ppp) REVERT: E 121 ASP cc_start: 0.8485 (t0) cc_final: 0.8158 (t0) REVERT: F 71 ARG cc_start: 0.8365 (tpt90) cc_final: 0.8045 (tpm170) REVERT: F 83 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8167 (pmm) REVERT: F 98 MET cc_start: 0.8593 (tmm) cc_final: 0.8207 (tmm) REVERT: F 181 ASP cc_start: 0.8608 (m-30) cc_final: 0.7995 (t0) REVERT: F 185 MET cc_start: 0.8570 (ptp) cc_final: 0.8184 (ppp) REVERT: F 192 TYR cc_start: 0.8631 (m-80) cc_final: 0.8265 (m-80) outliers start: 42 outliers final: 29 residues processed: 310 average time/residue: 0.2391 time to fit residues: 108.2297 Evaluate side-chains 294 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 99 HIS A 172 HIS ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.088601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073669 restraints weight = 35303.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075693 restraints weight = 19984.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.077086 restraints weight = 13580.047| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8994 Z= 0.195 Angle : 0.751 14.445 12273 Z= 0.354 Chirality : 0.048 0.326 1454 Planarity : 0.004 0.053 1519 Dihedral : 4.815 24.299 1206 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.25 % Favored : 92.67 % Rotamer: Outliers : 4.47 % Allowed : 21.37 % Favored : 74.15 % 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 (0.26), residues: 1118 helix: 0.51 (0.20), residues: 680 sheet: -0.73 (0.78), residues: 52 loop : -2.15 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 123 HIS 0.008 0.001 HIS A 96 PHE 0.028 0.001 PHE F 28 TYR 0.027 0.001 TYR C 139 ARG 0.004 0.000 ARG F 216 *********************** 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 313 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8739 (tp) cc_final: 0.8538 (mp) REVERT: A 78 TRP cc_start: 0.8147 (t60) cc_final: 0.7883 (t60) REVERT: B 31 VAL cc_start: 0.9386 (t) cc_final: 0.9121 (p) REVERT: B 100 HIS cc_start: 0.8348 (t70) cc_final: 0.8082 (t70) REVERT: B 135 LEU cc_start: 0.9140 (mt) cc_final: 0.8653 (tt) REVERT: B 177 THR cc_start: 0.7862 (p) cc_final: 0.7502 (t) REVERT: B 185 MET cc_start: 0.8029 (ppp) cc_final: 0.7682 (ppp) REVERT: C 54 TYR cc_start: 0.7653 (t80) cc_final: 0.7139 (t80) REVERT: C 70 ILE cc_start: 0.9219 (tp) cc_final: 0.8870 (tp) REVERT: C 198 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7438 (mtm) REVERT: D 1 MET cc_start: -0.0319 (tpt) cc_final: -0.2536 (pmm) REVERT: D 41 MET cc_start: 0.8498 (ppp) cc_final: 0.8190 (ppp) REVERT: E 121 ASP cc_start: 0.8473 (t0) cc_final: 0.8127 (t0) REVERT: F 71 ARG cc_start: 0.8314 (tpt90) cc_final: 0.8016 (tpm170) REVERT: F 83 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8102 (pmm) REVERT: F 98 MET cc_start: 0.8424 (tmm) cc_final: 0.8177 (tmm) REVERT: F 132 THR cc_start: 0.8792 (t) cc_final: 0.8531 (p) REVERT: F 181 ASP cc_start: 0.8595 (m-30) cc_final: 0.7983 (t0) REVERT: F 185 MET cc_start: 0.8546 (ptp) cc_final: 0.8169 (ppp) outliers start: 41 outliers final: 33 residues processed: 292 average time/residue: 0.2191 time to fit residues: 93.8535 Evaluate side-chains 295 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 223 ASN ** 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 = 0.3685 r_free = 0.3685 target = 0.087969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.072876 restraints weight = 35675.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.074855 restraints weight = 20551.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.076226 restraints weight = 14179.149| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8994 Z= 0.203 Angle : 0.750 14.553 12273 Z= 0.356 Chirality : 0.047 0.333 1454 Planarity : 0.005 0.055 1519 Dihedral : 4.791 23.967 1206 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.69 % Favored : 92.22 % Rotamer: Outliers : 4.80 % Allowed : 24.10 % Favored : 71.10 % 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: -0.75 (0.26), residues: 1118 helix: 0.44 (0.20), residues: 679 sheet: -0.70 (0.77), residues: 52 loop : -2.14 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 60 HIS 0.006 0.001 HIS A 99 PHE 0.022 0.001 PHE F 28 TYR 0.016 0.001 TYR C 139 ARG 0.003 0.000 ARG F 216 *********************** 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 308 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8782 (tp) cc_final: 0.8573 (mp) REVERT: A 181 LEU cc_start: 0.9232 (mp) cc_final: 0.8993 (mp) REVERT: B 31 VAL cc_start: 0.9426 (t) cc_final: 0.9188 (p) REVERT: B 94 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8999 (mt) REVERT: B 100 HIS cc_start: 0.8423 (t70) cc_final: 0.8158 (t70) REVERT: B 135 LEU cc_start: 0.9241 (mt) cc_final: 0.8765 (tt) REVERT: B 177 THR cc_start: 0.7851 (p) cc_final: 0.7588 (t) REVERT: B 185 MET cc_start: 0.8098 (ppp) cc_final: 0.7661 (ppp) REVERT: C 54 TYR cc_start: 0.7708 (t80) cc_final: 0.7212 (t80) REVERT: C 70 ILE cc_start: 0.9318 (tp) cc_final: 0.9026 (tp) REVERT: C 74 MET cc_start: 0.8733 (mmm) cc_final: 0.8357 (mtt) REVERT: C 219 MET cc_start: 0.7659 (tpp) cc_final: 0.7408 (tpp) REVERT: D 1 MET cc_start: -0.0403 (tpt) cc_final: -0.2509 (pmm) REVERT: D 41 MET cc_start: 0.8515 (ppp) cc_final: 0.8189 (ppp) REVERT: E 121 ASP cc_start: 0.8486 (t0) cc_final: 0.8143 (t0) REVERT: F 71 ARG cc_start: 0.8334 (tpt90) cc_final: 0.8011 (tpm170) REVERT: F 83 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8160 (pmm) REVERT: F 98 MET cc_start: 0.8362 (tmm) cc_final: 0.8090 (tmm) REVERT: F 132 THR cc_start: 0.8819 (t) cc_final: 0.8554 (p) REVERT: F 181 ASP cc_start: 0.8653 (m-30) cc_final: 0.8050 (t0) REVERT: F 185 MET cc_start: 0.8557 (ptp) cc_final: 0.8131 (ppp) outliers start: 44 outliers final: 35 residues processed: 283 average time/residue: 0.1764 time to fit residues: 72.4450 Evaluate side-chains 288 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.085815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.070968 restraints weight = 35784.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.072932 restraints weight = 20479.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.074271 restraints weight = 14006.517| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8994 Z= 0.249 Angle : 0.767 13.560 12273 Z= 0.367 Chirality : 0.048 0.342 1454 Planarity : 0.005 0.055 1519 Dihedral : 4.876 24.015 1206 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.14 % Favored : 91.77 % Rotamer: Outliers : 5.78 % Allowed : 24.75 % Favored : 69.47 % 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: -0.87 (0.25), residues: 1118 helix: 0.34 (0.20), residues: 687 sheet: -1.02 (0.74), residues: 52 loop : -2.19 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 123 HIS 0.006 0.001 HIS A 172 PHE 0.035 0.002 PHE B 142 TYR 0.025 0.002 TYR C 139 ARG 0.004 0.000 ARG F 216 *********************** 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 303 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 250 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.9261 (mp) cc_final: 0.9058 (tp) REVERT: B 31 VAL cc_start: 0.9446 (t) cc_final: 0.9180 (p) REVERT: B 75 GLN cc_start: 0.9310 (pm20) cc_final: 0.9077 (pm20) REVERT: B 135 LEU cc_start: 0.9297 (mt) cc_final: 0.8829 (tt) REVERT: B 177 THR cc_start: 0.7828 (p) cc_final: 0.7573 (t) REVERT: B 185 MET cc_start: 0.8085 (ppp) cc_final: 0.7663 (ppp) REVERT: C 54 TYR cc_start: 0.7786 (t80) cc_final: 0.7352 (t80) REVERT: C 70 ILE cc_start: 0.9240 (tp) cc_final: 0.8959 (tp) REVERT: C 74 MET cc_start: 0.8720 (mmm) cc_final: 0.8520 (mtt) REVERT: C 219 MET cc_start: 0.7814 (tpp) cc_final: 0.7481 (tpp) REVERT: C 230 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8817 (pttm) REVERT: D 1 MET cc_start: 0.0024 (tpt) cc_final: -0.1984 (pmm) REVERT: D 41 MET cc_start: 0.8520 (ppp) cc_final: 0.8104 (ppp) REVERT: F 83 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8210 (pmm) REVERT: F 98 MET cc_start: 0.8404 (tmm) cc_final: 0.8011 (tmm) REVERT: F 132 THR cc_start: 0.8903 (t) cc_final: 0.8654 (p) REVERT: F 181 ASP cc_start: 0.8706 (m-30) cc_final: 0.8127 (t0) REVERT: F 185 MET cc_start: 0.8518 (ptp) cc_final: 0.8134 (ppp) REVERT: F 192 TYR cc_start: 0.8765 (m-80) cc_final: 0.8472 (m-80) outliers start: 53 outliers final: 41 residues processed: 281 average time/residue: 0.1667 time to fit residues: 68.6562 Evaluate side-chains 286 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 0.0670 chunk 46 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 8 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 0.0980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS F 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.089130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074139 restraints weight = 35782.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.076136 restraints weight = 20265.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.077481 restraints weight = 13827.283| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8994 Z= 0.179 Angle : 0.782 13.737 12273 Z= 0.360 Chirality : 0.047 0.291 1454 Planarity : 0.004 0.055 1519 Dihedral : 4.811 23.813 1206 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 4.47 % Allowed : 27.15 % Favored : 68.38 % 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: -0.76 (0.26), residues: 1118 helix: 0.40 (0.20), residues: 689 sheet: -0.68 (0.76), residues: 52 loop : -2.13 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 60 HIS 0.006 0.001 HIS A 99 PHE 0.030 0.001 PHE B 142 TYR 0.016 0.001 TYR B 124 ARG 0.004 0.000 ARG F 216 *********************** 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 318 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 277 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.7915 (tmm) cc_final: 0.6907 (tmm) REVERT: A 181 LEU cc_start: 0.9227 (mp) cc_final: 0.8934 (tp) REVERT: B 5 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8036 (mtm180) REVERT: B 75 GLN cc_start: 0.9272 (pm20) cc_final: 0.8927 (pm20) REVERT: B 96 LYS cc_start: 0.9345 (ttpt) cc_final: 0.9075 (ttpt) REVERT: B 122 ASP cc_start: 0.8277 (t0) cc_final: 0.7571 (t70) REVERT: B 135 LEU cc_start: 0.9280 (mt) cc_final: 0.8814 (tt) REVERT: B 170 ILE cc_start: 0.9289 (mm) cc_final: 0.9088 (mm) REVERT: B 177 THR cc_start: 0.7734 (p) cc_final: 0.7486 (t) REVERT: B 185 MET cc_start: 0.8073 (ppp) cc_final: 0.7638 (ppp) REVERT: C 54 TYR cc_start: 0.7785 (t80) cc_final: 0.7356 (t80) REVERT: C 70 ILE cc_start: 0.9245 (tp) cc_final: 0.8949 (tp) REVERT: C 71 TYR cc_start: 0.8773 (t80) cc_final: 0.8571 (t80) REVERT: C 219 MET cc_start: 0.7800 (tpp) cc_final: 0.7423 (tpp) REVERT: D 1 MET cc_start: 0.0093 (tpt) cc_final: -0.1939 (pmm) REVERT: D 41 MET cc_start: 0.8512 (ppp) cc_final: 0.8066 (ppp) REVERT: E 121 ASP cc_start: 0.8384 (t0) cc_final: 0.8143 (t0) REVERT: F 15 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: F 83 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8058 (pmm) REVERT: F 98 MET cc_start: 0.8361 (tmm) cc_final: 0.8084 (tmm) REVERT: F 132 THR cc_start: 0.8829 (t) cc_final: 0.8574 (p) REVERT: F 181 ASP cc_start: 0.8678 (m-30) cc_final: 0.8111 (t0) REVERT: F 185 MET cc_start: 0.8489 (ptp) cc_final: 0.8117 (ppp) outliers start: 41 outliers final: 28 residues processed: 299 average time/residue: 0.1693 time to fit residues: 72.7416 Evaluate side-chains 288 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 0.0010 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.088914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.073665 restraints weight = 36055.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.075728 restraints weight = 20495.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.077113 restraints weight = 14036.099| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8994 Z= 0.182 Angle : 0.791 13.379 12273 Z= 0.365 Chirality : 0.048 0.361 1454 Planarity : 0.005 0.059 1519 Dihedral : 4.747 23.183 1206 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 4.25 % Allowed : 29.01 % Favored : 66.74 % 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 (0.26), residues: 1118 helix: 0.37 (0.20), residues: 697 sheet: -0.49 (0.77), residues: 52 loop : -2.10 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 29 HIS 0.008 0.001 HIS E 66 PHE 0.029 0.001 PHE F 28 TYR 0.018 0.001 TYR C 139 ARG 0.005 0.000 ARG F 216 *********************** 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 298 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7768 (p90) cc_final: 0.7001 (m-10) REVERT: B 5 ARG cc_start: 0.8806 (mtm180) cc_final: 0.8063 (mtm180) REVERT: B 75 GLN cc_start: 0.9135 (pm20) cc_final: 0.8929 (pm20) REVERT: B 122 ASP cc_start: 0.8033 (t0) cc_final: 0.7503 (p0) REVERT: B 135 LEU cc_start: 0.9238 (mt) cc_final: 0.8799 (tt) REVERT: B 177 THR cc_start: 0.7703 (p) cc_final: 0.7437 (t) REVERT: B 185 MET cc_start: 0.8097 (ppp) cc_final: 0.7658 (ppp) REVERT: C 54 TYR cc_start: 0.7648 (t80) cc_final: 0.7211 (t80) REVERT: C 219 MET cc_start: 0.7630 (tpp) cc_final: 0.7275 (tpp) REVERT: D 1 MET cc_start: 0.0268 (tpt) cc_final: -0.1920 (pmm) REVERT: D 41 MET cc_start: 0.8536 (ppp) cc_final: 0.8093 (ppp) REVERT: E 121 ASP cc_start: 0.8336 (t0) cc_final: 0.8069 (t0) REVERT: F 15 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: F 83 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8029 (pmm) REVERT: F 98 MET cc_start: 0.8431 (tmm) cc_final: 0.8111 (tmm) REVERT: F 132 THR cc_start: 0.8735 (t) cc_final: 0.8485 (p) REVERT: F 181 ASP cc_start: 0.8599 (m-30) cc_final: 0.8048 (t0) REVERT: F 185 MET cc_start: 0.8401 (ptp) cc_final: 0.8069 (ppp) outliers start: 39 outliers final: 32 residues processed: 277 average time/residue: 0.1667 time to fit residues: 66.7692 Evaluate side-chains 290 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS F 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.088489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073359 restraints weight = 35914.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.075354 restraints weight = 20613.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.076705 restraints weight = 14170.225| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8994 Z= 0.188 Angle : 0.794 12.722 12273 Z= 0.366 Chirality : 0.048 0.351 1454 Planarity : 0.005 0.059 1519 Dihedral : 4.722 23.075 1206 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.16 % Favored : 92.75 % Rotamer: Outliers : 3.82 % Allowed : 30.10 % Favored : 66.09 % 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: -0.70 (0.26), residues: 1118 helix: 0.37 (0.20), residues: 698 sheet: -0.33 (0.78), residues: 52 loop : -2.07 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 60 HIS 0.008 0.001 HIS E 66 PHE 0.029 0.001 PHE F 28 TYR 0.021 0.001 TYR C 139 ARG 0.005 0.000 ARG F 216 *********************** 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 293 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7891 (p90) cc_final: 0.7081 (m-80) REVERT: B 75 GLN cc_start: 0.9173 (pm20) cc_final: 0.8952 (pm20) REVERT: B 96 LYS cc_start: 0.9391 (ttpt) cc_final: 0.9103 (ttpt) REVERT: B 121 MET cc_start: 0.6347 (ttp) cc_final: 0.5995 (tmm) REVERT: B 122 ASP cc_start: 0.8531 (t0) cc_final: 0.8314 (t0) REVERT: B 135 LEU cc_start: 0.9292 (mt) cc_final: 0.8853 (tt) REVERT: B 177 THR cc_start: 0.7650 (p) cc_final: 0.7404 (t) REVERT: C 54 TYR cc_start: 0.7676 (t80) cc_final: 0.7258 (t80) REVERT: C 219 MET cc_start: 0.7709 (tpp) cc_final: 0.7313 (tpp) REVERT: D 1 MET cc_start: 0.0220 (tpt) cc_final: -0.1920 (pmm) REVERT: D 41 MET cc_start: 0.8546 (ppp) cc_final: 0.8091 (ppp) REVERT: F 15 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: F 83 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8124 (pmm) REVERT: F 98 MET cc_start: 0.8494 (tmm) cc_final: 0.8152 (tmm) REVERT: F 132 THR cc_start: 0.8802 (t) cc_final: 0.8550 (p) REVERT: F 181 ASP cc_start: 0.8643 (m-30) cc_final: 0.8087 (t0) REVERT: F 185 MET cc_start: 0.8401 (ptp) cc_final: 0.8057 (ppp) outliers start: 35 outliers final: 31 residues processed: 276 average time/residue: 0.1646 time to fit residues: 65.7438 Evaluate side-chains 283 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 68 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 90 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.088059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.073098 restraints weight = 35790.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.075088 restraints weight = 20334.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.076508 restraints weight = 13941.665| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8994 Z= 0.198 Angle : 0.822 12.515 12273 Z= 0.379 Chirality : 0.049 0.345 1454 Planarity : 0.005 0.060 1519 Dihedral : 4.738 23.079 1206 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer: Outliers : 3.60 % Allowed : 30.21 % Favored : 66.19 % 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: -0.73 (0.26), residues: 1118 helix: 0.35 (0.20), residues: 697 sheet: -0.29 (0.79), residues: 52 loop : -2.08 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 60 HIS 0.008 0.001 HIS E 66 PHE 0.028 0.001 PHE F 28 TYR 0.019 0.001 TYR C 139 ARG 0.004 0.000 ARG F 216 ********************** 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 285 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7813 (p90) cc_final: 0.6983 (m-80) REVERT: B 121 MET cc_start: 0.6285 (ttp) cc_final: 0.5966 (tmm) REVERT: B 122 ASP cc_start: 0.8547 (t0) cc_final: 0.8263 (t0) REVERT: B 135 LEU cc_start: 0.9293 (mt) cc_final: 0.8867 (tt) REVERT: B 177 THR cc_start: 0.7615 (p) cc_final: 0.7364 (t) REVERT: B 185 MET cc_start: 0.8071 (ppp) cc_final: 0.7742 (ppp) REVERT: C 54 TYR cc_start: 0.7659 (t80) cc_final: 0.7263 (t80) REVERT: C 74 MET cc_start: 0.8814 (mmm) cc_final: 0.8458 (mtt) REVERT: C 219 MET cc_start: 0.7670 (tpp) cc_final: 0.7290 (tpp) REVERT: D 1 MET cc_start: 0.0143 (tpt) cc_final: -0.1952 (pmm) REVERT: D 41 MET cc_start: 0.8597 (ppp) cc_final: 0.8120 (ppp) REVERT: F 15 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: F 71 ARG cc_start: 0.8340 (tpt170) cc_final: 0.7960 (tpm170) REVERT: F 83 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8117 (pmm) REVERT: F 98 MET cc_start: 0.8504 (tmm) cc_final: 0.8170 (tmm) REVERT: F 132 THR cc_start: 0.8804 (t) cc_final: 0.8544 (p) REVERT: F 181 ASP cc_start: 0.8657 (m-30) cc_final: 0.8101 (t0) REVERT: F 185 MET cc_start: 0.8375 (ptp) cc_final: 0.8074 (ppp) outliers start: 33 outliers final: 29 residues processed: 269 average time/residue: 0.1808 time to fit residues: 71.2650 Evaluate side-chains 278 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 0.0170 chunk 103 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS C 223 ASN E 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.088096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073238 restraints weight = 35636.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.075243 restraints weight = 20275.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.076616 restraints weight = 13792.278| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8994 Z= 0.200 Angle : 0.847 13.508 12273 Z= 0.389 Chirality : 0.049 0.339 1454 Planarity : 0.005 0.059 1519 Dihedral : 4.784 23.083 1206 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer: Outliers : 3.71 % Allowed : 30.86 % Favored : 65.43 % 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: -0.73 (0.26), residues: 1118 helix: 0.36 (0.20), residues: 697 sheet: -0.48 (0.80), residues: 52 loop : -2.07 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 60 HIS 0.006 0.001 HIS A 99 PHE 0.029 0.001 PHE F 28 TYR 0.015 0.001 TYR C 139 ARG 0.004 0.000 ARG F 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2994.21 seconds wall clock time: 54 minutes 12.48 seconds (3252.48 seconds total)