Starting phenix.real_space_refine on Mon Mar 11 17:43:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/03_2024/7vfj_31956.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/03_2024/7vfj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/03_2024/7vfj_31956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/03_2024/7vfj_31956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/03_2024/7vfj_31956.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/03_2024/7vfj_31956.pdb" } 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 Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 5.14, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.7 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: 0.81 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: 2.28 Time building geometry restraints manager: 3.81 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: 94.96 - 102.79: 60 102.79 - 110.63: 2782 110.63 - 118.46: 4343 118.46 - 126.30: 4848 126.30 - 134.13: 240 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 2.520 nonbonded pdb=" OG1 THR A 90 " pdb=" OE1 GLU A 93 " model vdw 2.190 2.440 nonbonded pdb=" OG1 THR A 146 " pdb=" O GLY A 176 " model vdw 2.192 2.440 nonbonded pdb=" O VAL F 159 " pdb=" OG SER F 162 " model vdw 2.222 2.440 nonbonded pdb=" NE2 HIS E 99 " pdb=" O ASP E 101 " model vdw 2.239 2.520 ... (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 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: 1.970 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: 7.210 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 26.570 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.100 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.043 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: 0.1711 time to fit residues: 79.4171 Evaluate side-chains 267 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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: 6.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8994 Z= 0.281 Angle : 0.772 8.791 12273 Z= 0.380 Chirality : 0.046 0.297 1454 Planarity : 0.005 0.047 1519 Dihedral : 4.993 28.527 1206 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.59 % Favored : 91.14 % Rotamer: Outliers : 3.49 % Allowed : 16.36 % Favored : 80.15 % 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: -1.04 (0.26), residues: 1118 helix: 0.23 (0.21), residues: 680 sheet: -0.99 (0.74), residues: 52 loop : -2.29 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 29 HIS 0.008 0.001 HIS A 99 PHE 0.030 0.002 PHE A 97 TYR 0.020 0.002 TYR C 139 ARG 0.007 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 311 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8662 (tp) cc_final: 0.8409 (mp) REVERT: A 88 ARG cc_start: 0.8633 (ptp90) cc_final: 0.8214 (ttm110) REVERT: B 31 VAL cc_start: 0.9391 (t) cc_final: 0.9168 (p) REVERT: B 135 LEU cc_start: 0.9093 (mt) cc_final: 0.8594 (tt) REVERT: C 25 LEU cc_start: 0.9584 (tp) cc_final: 0.9382 (tp) REVERT: C 70 ILE cc_start: 0.9331 (tp) cc_final: 0.9059 (tp) REVERT: C 139 TYR cc_start: 0.8683 (m-10) cc_final: 0.8433 (m-10) REVERT: C 221 MET cc_start: 0.8829 (tpt) cc_final: 0.8491 (tpt) REVERT: D 1 MET cc_start: -0.0660 (tpt) cc_final: -0.2719 (pmm) REVERT: D 41 MET cc_start: 0.8530 (ppp) cc_final: 0.8295 (ppp) REVERT: E 121 ASP cc_start: 0.8529 (t0) cc_final: 0.8238 (t0) REVERT: F 17 HIS cc_start: 0.7793 (t-90) cc_final: 0.7522 (t-90) REVERT: F 83 MET cc_start: 0.8537 (pmm) cc_final: 0.8224 (pmm) REVERT: F 181 ASP cc_start: 0.8612 (m-30) cc_final: 0.7910 (t0) REVERT: F 192 TYR cc_start: 0.8642 (m-80) cc_final: 0.8137 (m-80) outliers start: 32 outliers final: 22 residues processed: 295 average time/residue: 0.1645 time to fit residues: 70.1467 Evaluate side-chains 279 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 257 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 146 THR 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 72 ASP Chi-restraints excluded: chain B residue 73 ASP 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 E residue 163 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 81 GLN 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 172 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** A 99 HIS C 16 GLN E 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8994 Z= 0.309 Angle : 0.788 11.090 12273 Z= 0.385 Chirality : 0.047 0.297 1454 Planarity : 0.005 0.048 1519 Dihedral : 5.123 25.679 1206 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.14 % Favored : 91.59 % Rotamer: Outliers : 6.54 % Allowed : 18.10 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1118 helix: 0.28 (0.20), residues: 679 sheet: -1.30 (0.74), residues: 52 loop : -2.33 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 123 HIS 0.005 0.001 HIS C 174 PHE 0.024 0.002 PHE A 97 TYR 0.015 0.002 TYR C 139 ARG 0.005 0.001 ARG F 156 *********************** 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 327 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 267 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8727 (tp) cc_final: 0.8454 (mp) REVERT: A 78 TRP cc_start: 0.8307 (t60) cc_final: 0.8013 (t60) REVERT: A 148 TRP cc_start: 0.7411 (m-10) cc_final: 0.7201 (m-10) REVERT: A 169 MET cc_start: 0.7951 (tpt) cc_final: 0.7661 (tpp) REVERT: B 2 MET cc_start: 0.6489 (ttm) cc_final: 0.6270 (ttp) REVERT: B 31 VAL cc_start: 0.9489 (t) cc_final: 0.9248 (p) REVERT: B 94 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9107 (mt) REVERT: B 135 LEU cc_start: 0.9153 (mt) cc_final: 0.8619 (tt) REVERT: B 177 THR cc_start: 0.7973 (p) cc_final: 0.7591 (t) REVERT: B 185 MET cc_start: 0.8146 (ppp) cc_final: 0.7826 (ppp) REVERT: C 54 TYR cc_start: 0.7908 (t80) cc_final: 0.7506 (t80) REVERT: C 70 ILE cc_start: 0.9251 (tp) cc_final: 0.8885 (tp) REVERT: C 221 MET cc_start: 0.8884 (tpt) cc_final: 0.8533 (tpt) REVERT: D 1 MET cc_start: -0.0476 (tpt) cc_final: -0.2443 (pmm) REVERT: D 41 MET cc_start: 0.8546 (ppp) cc_final: 0.8273 (ppp) REVERT: E 121 ASP cc_start: 0.8516 (t0) cc_final: 0.8245 (t0) REVERT: F 17 HIS cc_start: 0.7859 (t-90) cc_final: 0.7598 (t-90) REVERT: F 83 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8359 (pmm) REVERT: F 98 MET cc_start: 0.8596 (tmm) cc_final: 0.8209 (tmm) REVERT: F 181 ASP cc_start: 0.8732 (m-30) cc_final: 0.8137 (t0) REVERT: F 185 MET cc_start: 0.8596 (ptp) cc_final: 0.8232 (ppp) REVERT: F 192 TYR cc_start: 0.8742 (m-80) cc_final: 0.8445 (m-80) outliers start: 60 outliers final: 44 residues processed: 295 average time/residue: 0.1659 time to fit residues: 70.5681 Evaluate side-chains 293 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 247 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 146 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain B residue 7 PHE 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 72 ASP 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 118 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 26 VAL 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 75 ASN Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ASP 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 131 LEU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 177 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3205 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= 0.277 Angle : 0.769 12.034 12273 Z= 0.370 Chirality : 0.047 0.294 1454 Planarity : 0.005 0.048 1519 Dihedral : 5.067 24.801 1206 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.41 % Favored : 91.32 % Rotamer: Outliers : 7.09 % Allowed : 22.46 % Favored : 70.45 % 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: -0.94 (0.26), residues: 1118 helix: 0.36 (0.20), residues: 679 sheet: -1.33 (0.74), residues: 52 loop : -2.28 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 123 HIS 0.012 0.001 HIS A 96 PHE 0.021 0.002 PHE F 28 TYR 0.026 0.002 TYR C 139 ARG 0.003 0.000 ARG A 133 *********************** 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 326 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 261 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8712 (tp) cc_final: 0.8479 (mp) REVERT: A 78 TRP cc_start: 0.8321 (t60) cc_final: 0.8090 (t60) REVERT: B 2 MET cc_start: 0.6477 (ttm) cc_final: 0.6270 (ttm) REVERT: B 31 VAL cc_start: 0.9487 (t) cc_final: 0.9237 (p) REVERT: B 94 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9135 (mt) REVERT: B 135 LEU cc_start: 0.9169 (mt) cc_final: 0.8649 (tt) REVERT: B 177 THR cc_start: 0.7979 (p) cc_final: 0.7726 (t) REVERT: C 54 TYR cc_start: 0.7898 (t80) cc_final: 0.7552 (t80) REVERT: C 70 ILE cc_start: 0.9224 (tp) cc_final: 0.8878 (tp) REVERT: C 74 MET cc_start: 0.8458 (mtt) cc_final: 0.8061 (mtt) REVERT: C 198 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7595 (mmm) REVERT: C 221 MET cc_start: 0.8862 (tpt) cc_final: 0.8517 (tpt) REVERT: D 1 MET cc_start: -0.0164 (tpt) cc_final: -0.1938 (pmm) REVERT: D 41 MET cc_start: 0.8541 (ppp) cc_final: 0.8246 (ppp) REVERT: E 60 TRP cc_start: 0.8997 (OUTLIER) cc_final: 0.7871 (t-100) REVERT: E 121 ASP cc_start: 0.8536 (t0) cc_final: 0.8249 (t0) REVERT: F 15 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: F 17 HIS cc_start: 0.7958 (t-90) cc_final: 0.7685 (t-90) REVERT: F 83 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8265 (pmm) REVERT: F 98 MET cc_start: 0.8568 (tmm) cc_final: 0.8075 (tmm) REVERT: F 181 ASP cc_start: 0.8712 (m-30) cc_final: 0.8119 (t0) REVERT: F 185 MET cc_start: 0.8546 (ptp) cc_final: 0.8204 (ppp) REVERT: F 192 TYR cc_start: 0.8811 (m-80) cc_final: 0.8500 (m-80) outliers start: 65 outliers final: 49 residues processed: 297 average time/residue: 0.1616 time to fit residues: 69.9075 Evaluate side-chains 304 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 250 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 146 THR 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 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 72 ASP 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 134 LEU Chi-restraints excluded: chain B residue 143 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 B residue 200 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 60 TRP Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ASP 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 Chi-restraints excluded: chain F residue 177 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.0470 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.0010 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.0870 overall best weight: 0.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS 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 167 GLN E 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3365 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= 0.180 Angle : 0.746 12.432 12273 Z= 0.348 Chirality : 0.047 0.288 1454 Planarity : 0.004 0.050 1519 Dihedral : 4.768 24.204 1206 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.89 % Favored : 92.84 % Rotamer: Outliers : 5.45 % Allowed : 25.74 % Favored : 68.81 % 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: -0.79 (0.26), residues: 1118 helix: 0.47 (0.20), residues: 687 sheet: -1.10 (0.76), residues: 52 loop : -2.27 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 234 HIS 0.009 0.001 HIS A 96 PHE 0.023 0.001 PHE F 28 TYR 0.024 0.002 TYR C 139 ARG 0.005 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 330 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 280 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7788 (p90) cc_final: 0.6637 (m-10) REVERT: A 60 TRP cc_start: 0.6142 (t60) cc_final: 0.5348 (t60) REVERT: B 94 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9025 (mt) REVERT: B 100 HIS cc_start: 0.8573 (t70) cc_final: 0.8351 (t70) REVERT: B 135 LEU cc_start: 0.9196 (mt) cc_final: 0.8796 (tt) REVERT: B 177 THR cc_start: 0.7773 (p) cc_final: 0.7496 (t) REVERT: B 185 MET cc_start: 0.8017 (ppp) cc_final: 0.7691 (ppp) REVERT: C 50 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8058 (mm-40) REVERT: C 54 TYR cc_start: 0.7693 (t80) cc_final: 0.7399 (t80) REVERT: C 70 ILE cc_start: 0.9151 (tp) cc_final: 0.8794 (tp) REVERT: D 1 MET cc_start: -0.0024 (tpt) cc_final: -0.1882 (pmm) REVERT: D 41 MET cc_start: 0.8480 (ppp) cc_final: 0.8147 (ppp) REVERT: E 121 ASP cc_start: 0.8512 (t0) cc_final: 0.8225 (t0) REVERT: F 15 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: F 17 HIS cc_start: 0.7883 (t-90) cc_final: 0.7610 (t-90) REVERT: F 83 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7975 (pmm) REVERT: F 181 ASP cc_start: 0.8590 (m-30) cc_final: 0.7982 (t0) REVERT: F 185 MET cc_start: 0.8521 (ptp) cc_final: 0.8176 (ppp) REVERT: F 192 TYR cc_start: 0.8658 (m-80) cc_final: 0.8444 (m-80) outliers start: 50 outliers final: 32 residues processed: 303 average time/residue: 0.1637 time to fit residues: 71.7495 Evaluate side-chains 289 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 253 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 A residue 198 SER 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 37 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 118 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 50 GLN 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 75 ASN Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS C 184 HIS ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8994 Z= 0.290 Angle : 0.811 11.477 12273 Z= 0.386 Chirality : 0.049 0.291 1454 Planarity : 0.005 0.053 1519 Dihedral : 5.050 23.935 1206 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.94 % Favored : 90.88 % Rotamer: Outliers : 6.43 % Allowed : 27.48 % 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: -0.85 (0.26), residues: 1118 helix: 0.41 (0.20), residues: 677 sheet: -1.04 (0.77), residues: 52 loop : -2.20 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 123 HIS 0.007 0.001 HIS A 96 PHE 0.029 0.002 PHE F 28 TYR 0.029 0.002 TYR C 139 ARG 0.004 0.001 ARG A 133 *********************** 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 306 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 247 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8754 (mppt) cc_final: 0.8545 (mppt) REVERT: B 31 VAL cc_start: 0.9533 (t) cc_final: 0.9287 (p) REVERT: B 135 LEU cc_start: 0.9319 (mt) cc_final: 0.8896 (tt) REVERT: B 177 THR cc_start: 0.7901 (p) cc_final: 0.7629 (t) REVERT: B 185 MET cc_start: 0.7989 (ppp) cc_final: 0.7571 (ppp) REVERT: C 54 TYR cc_start: 0.7924 (t80) cc_final: 0.7630 (t80) REVERT: C 70 ILE cc_start: 0.9241 (tp) cc_final: 0.8914 (tp) REVERT: D 1 MET cc_start: 0.0087 (tpt) cc_final: -0.1756 (pmm) REVERT: D 41 MET cc_start: 0.8538 (ppp) cc_final: 0.8159 (ppp) REVERT: E 60 TRP cc_start: 0.8944 (OUTLIER) cc_final: 0.8156 (t-100) REVERT: F 15 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: F 17 HIS cc_start: 0.7945 (t-90) cc_final: 0.7651 (t-90) REVERT: F 83 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8181 (pmm) REVERT: F 98 MET cc_start: 0.8499 (tmm) cc_final: 0.8219 (tmm) REVERT: F 181 ASP cc_start: 0.8740 (m-30) cc_final: 0.8114 (t0) REVERT: F 185 MET cc_start: 0.8540 (ptp) cc_final: 0.8233 (ppp) REVERT: F 192 TYR cc_start: 0.8819 (m-80) cc_final: 0.8592 (m-80) outliers start: 59 outliers final: 46 residues processed: 278 average time/residue: 0.1644 time to fit residues: 66.4929 Evaluate side-chains 287 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 238 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 146 THR 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 37 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 118 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 200 LEU Chi-restraints excluded: chain C residue 48 TYR 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 60 TRP Chi-restraints excluded: chain E residue 75 ASN 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 E residue 182 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ASP 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 155 LYS Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 177 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS C 223 ASN ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3950 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= 0.207 Angle : 0.798 13.162 12273 Z= 0.369 Chirality : 0.048 0.327 1454 Planarity : 0.004 0.049 1519 Dihedral : 4.917 23.855 1206 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.96 % Favored : 91.86 % Rotamer: Outliers : 5.45 % Allowed : 29.12 % 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: -0.84 (0.25), residues: 1118 helix: 0.38 (0.20), residues: 684 sheet: -0.92 (0.77), residues: 52 loop : -2.20 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 55 HIS 0.007 0.001 HIS A 96 PHE 0.029 0.002 PHE F 28 TYR 0.020 0.002 TYR C 139 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 303 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 253 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 VAL cc_start: 0.9494 (t) cc_final: 0.9256 (p) REVERT: B 121 MET cc_start: 0.6637 (ttp) cc_final: 0.6422 (tmm) REVERT: B 135 LEU cc_start: 0.9301 (mt) cc_final: 0.8917 (tt) REVERT: B 177 THR cc_start: 0.7784 (p) cc_final: 0.7529 (t) REVERT: B 185 MET cc_start: 0.7954 (ppp) cc_final: 0.7453 (ppp) REVERT: C 54 TYR cc_start: 0.7847 (t80) cc_final: 0.7545 (t80) REVERT: C 70 ILE cc_start: 0.9252 (tp) cc_final: 0.8981 (tp) REVERT: D 1 MET cc_start: 0.0020 (tpt) cc_final: -0.1747 (pmm) REVERT: D 41 MET cc_start: 0.8540 (ppp) cc_final: 0.8124 (ppp) REVERT: F 17 HIS cc_start: 0.7915 (t-90) cc_final: 0.7630 (t-90) REVERT: F 83 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8039 (pmm) REVERT: F 98 MET cc_start: 0.8446 (tmm) cc_final: 0.8133 (tmm) REVERT: F 181 ASP cc_start: 0.8662 (m-30) cc_final: 0.8064 (t0) REVERT: F 185 MET cc_start: 0.8494 (ptp) cc_final: 0.8177 (ppp) REVERT: F 192 TYR cc_start: 0.8733 (m-80) cc_final: 0.8497 (m-80) outliers start: 50 outliers final: 38 residues processed: 279 average time/residue: 0.1586 time to fit residues: 64.5744 Evaluate side-chains 283 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 244 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 146 THR 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 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 67 SER 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 75 ASN Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ASP 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 Chi-restraints excluded: chain F residue 177 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 16 GLN C 85 GLN C 184 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8994 Z= 0.205 Angle : 0.803 12.954 12273 Z= 0.369 Chirality : 0.048 0.315 1454 Planarity : 0.004 0.052 1519 Dihedral : 4.864 23.549 1206 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.14 % Favored : 91.68 % Rotamer: Outliers : 5.67 % Allowed : 29.88 % Favored : 64.45 % 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: -0.80 (0.25), residues: 1118 helix: 0.39 (0.20), residues: 684 sheet: -0.85 (0.76), residues: 52 loop : -2.13 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 101 HIS 0.006 0.001 HIS A 96 PHE 0.029 0.002 PHE F 28 TYR 0.020 0.001 TYR C 139 ARG 0.003 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 305 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 253 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 VAL cc_start: 0.9512 (t) cc_final: 0.9295 (p) REVERT: B 121 MET cc_start: 0.6723 (ttp) cc_final: 0.6353 (tmm) REVERT: B 135 LEU cc_start: 0.9324 (mt) cc_final: 0.8947 (tt) REVERT: B 177 THR cc_start: 0.7775 (p) cc_final: 0.7538 (t) REVERT: B 185 MET cc_start: 0.7925 (ppp) cc_final: 0.7494 (ppp) REVERT: C 54 TYR cc_start: 0.7817 (t80) cc_final: 0.7511 (t80) REVERT: C 70 ILE cc_start: 0.9253 (tp) cc_final: 0.8962 (tp) REVERT: D 1 MET cc_start: 0.0149 (tpt) cc_final: -0.1359 (pmm) REVERT: D 41 MET cc_start: 0.8520 (ppp) cc_final: 0.8103 (ppp) REVERT: E 60 TRP cc_start: 0.8841 (OUTLIER) cc_final: 0.7918 (t-100) REVERT: E 121 ASP cc_start: 0.8385 (t0) cc_final: 0.8165 (t0) REVERT: F 17 HIS cc_start: 0.7950 (t-90) cc_final: 0.7659 (t-90) REVERT: F 83 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7988 (pmm) REVERT: F 181 ASP cc_start: 0.8664 (m-30) cc_final: 0.8067 (t0) REVERT: F 185 MET cc_start: 0.8449 (ptp) cc_final: 0.8183 (ppp) REVERT: F 192 TYR cc_start: 0.8706 (m-80) cc_final: 0.8475 (m-80) outliers start: 52 outliers final: 44 residues processed: 279 average time/residue: 0.1816 time to fit residues: 73.0957 Evaluate side-chains 293 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 247 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 146 THR 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 29 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 143 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 67 SER 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 60 TRP Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ASP 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 Chi-restraints excluded: chain F residue 177 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 184 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8994 Z= 0.188 Angle : 0.810 12.868 12273 Z= 0.368 Chirality : 0.049 0.326 1454 Planarity : 0.004 0.048 1519 Dihedral : 4.781 23.448 1206 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.23 % Favored : 91.59 % Rotamer: Outliers : 5.02 % Allowed : 30.32 % Favored : 64.67 % 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: 0.37 (0.20), residues: 687 sheet: -0.78 (0.77), residues: 52 loop : -1.99 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 101 HIS 0.006 0.001 HIS A 96 PHE 0.029 0.001 PHE F 28 TYR 0.017 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 307 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 261 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 VAL cc_start: 0.9471 (t) cc_final: 0.9239 (p) REVERT: B 121 MET cc_start: 0.6753 (ttp) cc_final: 0.6435 (tmm) REVERT: B 135 LEU cc_start: 0.9311 (mt) cc_final: 0.8965 (tt) REVERT: B 177 THR cc_start: 0.7620 (p) cc_final: 0.7375 (t) REVERT: B 185 MET cc_start: 0.7937 (ppp) cc_final: 0.7471 (ppp) REVERT: C 54 TYR cc_start: 0.7798 (t80) cc_final: 0.7508 (t80) REVERT: C 70 ILE cc_start: 0.9201 (tp) cc_final: 0.8995 (tp) REVERT: D 1 MET cc_start: 0.0520 (tpt) cc_final: -0.0934 (pmm) REVERT: D 41 MET cc_start: 0.8516 (ppp) cc_final: 0.8104 (ppp) REVERT: F 17 HIS cc_start: 0.7911 (t-90) cc_final: 0.7628 (t-90) REVERT: F 83 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7929 (pmm) REVERT: F 98 MET cc_start: 0.8397 (tmm) cc_final: 0.8166 (tmm) REVERT: F 181 ASP cc_start: 0.8629 (m-30) cc_final: 0.8035 (t0) REVERT: F 185 MET cc_start: 0.8417 (ptp) cc_final: 0.8147 (ppp) REVERT: F 192 TYR cc_start: 0.8679 (m-80) cc_final: 0.8348 (m-80) outliers start: 46 outliers final: 40 residues processed: 282 average time/residue: 0.1634 time to fit residues: 66.7714 Evaluate side-chains 295 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 254 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 146 THR 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 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 ASP 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 67 SER 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 75 ASN Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 76 ASP 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 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 64 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 184 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4336 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= 0.222 Angle : 0.830 14.087 12273 Z= 0.380 Chirality : 0.049 0.341 1454 Planarity : 0.004 0.051 1519 Dihedral : 4.858 23.384 1206 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.32 % Favored : 91.50 % Rotamer: Outliers : 5.13 % Allowed : 30.64 % Favored : 64.23 % 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: -0.77 (0.26), residues: 1118 helix: 0.34 (0.20), residues: 686 sheet: -0.77 (0.77), residues: 52 loop : -2.00 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 101 HIS 0.006 0.001 HIS A 96 PHE 0.028 0.002 PHE F 28 TYR 0.022 0.001 TYR C 139 ARG 0.005 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 306 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 259 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 VAL cc_start: 0.9484 (t) cc_final: 0.9259 (p) REVERT: B 121 MET cc_start: 0.6778 (ttp) cc_final: 0.6465 (tmm) REVERT: B 135 LEU cc_start: 0.9362 (mt) cc_final: 0.8989 (tt) REVERT: B 177 THR cc_start: 0.7703 (p) cc_final: 0.7485 (t) REVERT: B 185 MET cc_start: 0.7947 (ppp) cc_final: 0.7456 (ppp) REVERT: C 54 TYR cc_start: 0.7856 (t80) cc_final: 0.7489 (t80) REVERT: D 1 MET cc_start: 0.0656 (tpt) cc_final: -0.0885 (pmm) REVERT: D 41 MET cc_start: 0.8532 (ppp) cc_final: 0.8115 (ppp) REVERT: E 86 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8631 (mmmm) REVERT: F 17 HIS cc_start: 0.7940 (t-90) cc_final: 0.7643 (t-90) REVERT: F 83 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7990 (pmm) REVERT: F 181 ASP cc_start: 0.8677 (m-30) cc_final: 0.8068 (t0) REVERT: F 185 MET cc_start: 0.8423 (ptp) cc_final: 0.8136 (ppp) REVERT: F 192 TYR cc_start: 0.8715 (m-80) cc_final: 0.8428 (m-80) outliers start: 47 outliers final: 40 residues processed: 280 average time/residue: 0.1815 time to fit residues: 73.9205 Evaluate side-chains 289 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 248 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 146 THR 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 37 LEU Chi-restraints excluded: chain B residue 72 ASP 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 67 SER 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 75 ASN Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 76 ASP 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 155 LYS Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 184 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.086429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071704 restraints weight = 35386.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.073660 restraints weight = 20157.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.074982 restraints weight = 13838.037| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4405 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= 0.194 Angle : 0.840 14.210 12273 Z= 0.381 Chirality : 0.049 0.325 1454 Planarity : 0.004 0.049 1519 Dihedral : 4.790 23.325 1206 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.23 % Favored : 91.59 % Rotamer: Outliers : 4.80 % Allowed : 31.52 % Favored : 63.69 % 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: 0.33 (0.20), residues: 683 sheet: -0.68 (0.78), residues: 52 loop : -1.92 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 60 HIS 0.006 0.001 HIS A 96 PHE 0.028 0.001 PHE F 28 TYR 0.015 0.001 TYR C 139 ARG 0.015 0.000 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.27 seconds wall clock time: 37 minutes 28.17 seconds (2248.17 seconds total)