Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 22:16:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/08_2023/7vfj_31956.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/08_2023/7vfj_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_31956/08_2023/7vfj_31956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/08_2023/7vfj_31956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/08_2023/7vfj_31956.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfj_31956/08_2023/7vfj_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-1.21rc1-5044/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: 4.64, per 1000 atoms: 0.53 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: 3.18 Conformation dependent library (CDL) restraints added in 1.4 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: 0.74 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: 2.03 Time building geometry restraints manager: 3.47 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: 1.860 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: 7.460 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 24.060 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.560 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1712 time to fit residues: 80.0960 Evaluate side-chains 266 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3089 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 8994 Z= 0.301 Angle : 0.788 8.530 12273 Z= 0.390 Chirality : 0.047 0.300 1454 Planarity : 0.005 0.045 1519 Dihedral : 5.047 28.982 1206 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.50 % Favored : 91.23 % Rotamer Outliers : 3.60 % 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: -1.07 (0.26), residues: 1118 helix: 0.21 (0.21), residues: 680 sheet: -0.99 (0.75), residues: 52 loop : -2.31 (0.31), residues: 386 *********************** 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: 33 poor density : 278 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 296 average time/residue: 0.1709 time to fit residues: 73.0575 Evaluate side-chains 279 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 255 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.0802 time to fit residues: 4.8165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.0370 chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 HIS ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8994 Z= 0.231 Angle : 0.746 10.223 12273 Z= 0.360 Chirality : 0.046 0.295 1454 Planarity : 0.005 0.048 1519 Dihedral : 4.953 25.178 1206 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.60 % Favored : 92.13 % Rotamer Outliers : 2.94 % 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: -0.96 (0.25), residues: 1118 helix: 0.33 (0.20), residues: 673 sheet: -1.09 (0.75), residues: 52 loop : -2.25 (0.31), residues: 393 *********************** 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 309 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 282 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 293 average time/residue: 0.1659 time to fit residues: 70.4072 Evaluate side-chains 277 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 259 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1023 time to fit residues: 4.4652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.0270 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2819 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= 0.188 Angle : 0.745 11.627 12273 Z= 0.347 Chirality : 0.046 0.326 1454 Planarity : 0.004 0.047 1519 Dihedral : 4.812 24.340 1206 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.69 % Favored : 92.04 % Rotamer Outliers : 3.05 % 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: -0.83 (0.26), residues: 1118 helix: 0.44 (0.20), residues: 684 sheet: -0.98 (0.75), residues: 52 loop : -2.29 (0.31), residues: 382 *********************** 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 312 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 293 average time/residue: 0.1645 time to fit residues: 69.6653 Evaluate side-chains 275 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 259 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0825 time to fit residues: 3.5654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3154 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= 0.212 Angle : 0.772 12.462 12273 Z= 0.363 Chirality : 0.047 0.339 1454 Planarity : 0.004 0.049 1519 Dihedral : 4.860 23.851 1206 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.69 % Favored : 92.13 % Rotamer Outliers : 2.62 % 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 (0.26), residues: 1118 helix: 0.43 (0.20), residues: 683 sheet: -0.77 (0.76), residues: 52 loop : -2.24 (0.32), residues: 383 *********************** 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 303 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 279 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 289 average time/residue: 0.1644 time to fit residues: 69.0061 Evaluate side-chains 274 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 260 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1060 time to fit residues: 3.7672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 0.0070 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8994 Z= 0.270 Angle : 0.805 12.453 12273 Z= 0.384 Chirality : 0.048 0.320 1454 Planarity : 0.005 0.048 1519 Dihedral : 4.958 23.496 1206 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.14 % Favored : 91.68 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.26), residues: 1118 helix: 0.36 (0.20), residues: 681 sheet: -0.92 (0.76), residues: 52 loop : -2.24 (0.31), residues: 385 *********************** 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 307 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 272 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 25 residues processed: 288 average time/residue: 0.1750 time to fit residues: 73.4000 Evaluate side-chains 281 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 256 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0879 time to fit residues: 5.1932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0980 chunk 61 optimal weight: 0.0870 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS C 223 ASN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3770 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= 0.199 Angle : 0.808 13.311 12273 Z= 0.376 Chirality : 0.047 0.297 1454 Planarity : 0.004 0.049 1519 Dihedral : 4.913 23.592 1206 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.05 % Favored : 91.77 % Rotamer Outliers : 1.85 % 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: -0.91 (0.25), residues: 1118 helix: 0.32 (0.20), residues: 678 sheet: -0.93 (0.75), residues: 52 loop : -2.18 (0.31), residues: 388 *********************** 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 289 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 272 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 279 average time/residue: 0.1674 time to fit residues: 67.6523 Evaluate side-chains 268 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 256 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1117 time to fit residues: 3.4660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 32 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3908 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= 0.194 Angle : 0.828 16.047 12273 Z= 0.382 Chirality : 0.048 0.335 1454 Planarity : 0.004 0.050 1519 Dihedral : 4.838 23.269 1206 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.87 % Favored : 91.95 % Rotamer Outliers : 1.20 % 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: -0.89 (0.25), residues: 1118 helix: 0.27 (0.20), residues: 680 sheet: -0.86 (0.75), residues: 52 loop : -2.07 (0.32), residues: 386 *********************** 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 273 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 262 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 266 average time/residue: 0.1724 time to fit residues: 66.8248 Evaluate side-chains 259 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 250 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0849 time to fit residues: 2.7200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 66 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8994 Z= 0.193 Angle : 0.829 14.256 12273 Z= 0.382 Chirality : 0.049 0.343 1454 Planarity : 0.004 0.049 1519 Dihedral : 4.791 22.921 1206 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.51 % Favored : 92.31 % Rotamer Outliers : 0.76 % 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: -0.83 (0.26), residues: 1118 helix: 0.31 (0.20), residues: 678 sheet: -0.54 (0.79), residues: 52 loop : -2.05 (0.32), residues: 388 *********************** 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 272 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 265 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 268 average time/residue: 0.1695 time to fit residues: 65.4858 Evaluate side-chains 258 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 253 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1576 time to fit residues: 2.4082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** 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: 0.7988 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8994 Z= 0.205 Angle : 0.855 13.845 12273 Z= 0.393 Chirality : 0.050 0.385 1454 Planarity : 0.004 0.049 1519 Dihedral : 4.803 22.881 1206 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.69 % Favored : 92.13 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1118 helix: 0.25 (0.20), residues: 679 sheet: -0.48 (0.80), residues: 52 loop : -2.03 (0.32), residues: 387 ********************** 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 257 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 254 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 257 average time/residue: 0.1678 time to fit residues: 62.3961 Evaluate side-chains 246 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0812 time to fit residues: 1.6759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.082578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.067795 restraints weight = 35200.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.069658 restraints weight = 20562.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070888 restraints weight = 14229.515| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 8994 Z= 0.316 Angle : 0.906 13.207 12273 Z= 0.431 Chirality : 0.052 0.355 1454 Planarity : 0.005 0.050 1519 Dihedral : 5.065 23.934 1206 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.23 % Favored : 91.59 % Rotamer Outliers : 1.20 % 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: -1.12 (0.25), residues: 1118 helix: 0.06 (0.20), residues: 679 sheet: -1.01 (0.75), residues: 52 loop : -2.09 (0.31), residues: 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1974.69 seconds wall clock time: 36 minutes 33.60 seconds (2193.60 seconds total)