Starting phenix.real_space_refine on Tue Mar 19 14:08:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2d_30955/03_2024/7e2d_30955.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2d_30955/03_2024/7e2d_30955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2d_30955/03_2024/7e2d_30955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2d_30955/03_2024/7e2d_30955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2d_30955/03_2024/7e2d_30955.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2d_30955/03_2024/7e2d_30955.pdb" } resolution = 3.71 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1092 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 14797 2.51 5 N 4041 2.21 5 O 4406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "F ARG 8": "NH1" <-> "NH2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "G ARG 263": "NH1" <-> "NH2" Residue "G ARG 277": "NH1" <-> "NH2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I ARG 816": "NH1" <-> "NH2" Residue "J GLU 519": "OE1" <-> "OE2" Residue "J ARG 555": "NH1" <-> "NH2" Residue "J ARG 600": "NH1" <-> "NH2" Residue "J GLU 627": "OE1" <-> "OE2" Residue "J PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 655": "NH1" <-> "NH2" Residue "J ARG 661": "NH1" <-> "NH2" Residue "J ARG 734": "NH1" <-> "NH2" Residue "J GLU 776": "OE1" <-> "OE2" Residue "J ARG 779": "NH1" <-> "NH2" Residue "J ARG 820": "NH1" <-> "NH2" Residue "J ARG 821": "NH1" <-> "NH2" Residue "J GLU 967": "OE1" <-> "OE2" Residue "J ARG 993": "NH1" <-> "NH2" Residue "J GLU 1014": "OE1" <-> "OE2" Residue "J ARG 1027": "NH1" <-> "NH2" Residue "J ARG 1035": "NH1" <-> "NH2" Residue "J GLU 1065": "OE1" <-> "OE2" Residue "J ARG 1097": "NH1" <-> "NH2" Residue "J GLU 1186": "OE1" <-> "OE2" Residue "J ARG 1229": "NH1" <-> "NH2" Residue "J GLU 1262": "OE1" <-> "OE2" Residue "K ARG 430": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23331 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1160 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "C" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1482 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "B" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1630 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1235 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1341 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 159} Chain breaks: 3 Chain: "F" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1470 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "G" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1648 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain breaks: 1 Chain: "H" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1180 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 138} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 4204 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 650} Link IDs: {'PTRANS': 16, 'TRANS': 771} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 2335 Unresolved non-hydrogen angles: 2973 Unresolved non-hydrogen dihedrals: 1927 Unresolved non-hydrogen chiralities: 228 Planarities with less than four sites: {'GLN:plan1': 30, 'ARG:plan': 24, 'TYR:plan': 22, 'ASN:plan1': 41, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 42, 'GLU:plan': 61, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 1235 Chain: "J" Number of atoms: 6332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6332 Classifications: {'peptide': 872} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 37, 'TRANS': 834} Chain breaks: 5 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 858 Unresolved non-hydrogen angles: 1097 Unresolved non-hydrogen dihedrals: 712 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 13, 'ASN:plan1': 16, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 419 Chain: "K" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1649 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 185 Time building chain proxies: 12.97, per 1000 atoms: 0.56 Number of scatterers: 23331 At special positions: 0 Unit cell: (190.925, 261.84, 130.92, 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 87 16.00 O 4406 8.00 N 4041 7.00 C 14797 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: 8.39 Conformation dependent library (CDL) restraints added in 4.4 seconds 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6336 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 32 sheets defined 36.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 removed outlier: 4.223A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 120 removed outlier: 3.996A pdb=" N ALA A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.979A pdb=" N TYR C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 75 removed outlier: 5.017A pdb=" N GLU C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 100 removed outlier: 4.038A pdb=" N SER C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS C 96 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 removed outlier: 3.824A pdb=" N CYS C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 removed outlier: 3.577A pdb=" N VAL C 155 " --> pdb=" O LEU C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 155' Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 112 through 139 removed outlier: 4.145A pdb=" N ARG B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 152 through 170 removed outlier: 4.097A pdb=" N ILE B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.895A pdb=" N LYS B 209 " --> pdb=" O ASN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'D' and resid 40 through 58 Processing helix chain 'D' and resid 99 through 110 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'E' and resid 31 through 50 removed outlier: 3.975A pdb=" N ILE E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA E 45 " --> pdb=" O HIS E 41 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 190 Processing helix chain 'E' and resid 204 through 219 removed outlier: 4.045A pdb=" N ASP E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU E 209 " --> pdb=" O ASN E 205 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 removed outlier: 5.073A pdb=" N GLU F 15 " --> pdb=" O LYS F 11 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 45 removed outlier: 3.580A pdb=" N TYR F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 4.078A pdb=" N VAL F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 93 through 98 removed outlier: 3.712A pdb=" N PHE F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 155 removed outlier: 3.750A pdb=" N GLY F 146 " --> pdb=" O ASN F 142 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 76 Processing helix chain 'G' and resid 79 through 107 removed outlier: 3.642A pdb=" N PHE G 83 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE G 94 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 192 removed outlier: 4.069A pdb=" N ILE G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G 180 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN G 181 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TRP G 188 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER G 189 " --> pdb=" O GLY G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 229 No H-bonds generated for 'chain 'G' and resid 227 through 229' Processing helix chain 'G' and resid 230 through 242 removed outlier: 4.164A pdb=" N CYS G 234 " --> pdb=" O GLU G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 245 No H-bonds generated for 'chain 'G' and resid 243 through 245' Processing helix chain 'G' and resid 271 through 281 removed outlier: 3.931A pdb=" N LEU G 275 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG G 277 " --> pdb=" O GLN G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 52 removed outlier: 4.213A pdb=" N GLU H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) Proline residue: H 38 - end of helix removed outlier: 3.572A pdb=" N LEU H 41 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP H 46 " --> pdb=" O HIS H 42 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 127 Processing helix chain 'H' and resid 129 through 146 Processing helix chain 'H' and resid 158 through 172 removed outlier: 3.609A pdb=" N ASP H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 269 Processing helix chain 'I' and resid 276 through 292 removed outlier: 3.703A pdb=" N TYR I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 317 removed outlier: 3.725A pdb=" N PHE I 309 " --> pdb=" O LEU I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 339 removed outlier: 4.003A pdb=" N SER I 336 " --> pdb=" O THR I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 369 removed outlier: 3.590A pdb=" N GLU I 350 " --> pdb=" O PRO I 346 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE I 351 " --> pdb=" O LEU I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 420 removed outlier: 4.010A pdb=" N GLU I 404 " --> pdb=" O THR I 400 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN I 405 " --> pdb=" O VAL I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 424 through 441 removed outlier: 3.635A pdb=" N VAL I 428 " --> pdb=" O ARG I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 452 Processing helix chain 'I' and resid 452 through 459 Processing helix chain 'I' and resid 466 through 481 removed outlier: 3.686A pdb=" N GLN I 473 " --> pdb=" O LEU I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 509 removed outlier: 3.898A pdb=" N PHE I 505 " --> pdb=" O LEU I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 514 No H-bonds generated for 'chain 'I' and resid 512 through 514' Processing helix chain 'I' and resid 515 through 529 removed outlier: 3.865A pdb=" N GLU I 519 " --> pdb=" O ASN I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 628 through 632 removed outlier: 4.145A pdb=" N GLY I 631 " --> pdb=" O ILE I 628 " (cutoff:3.500A) Processing helix chain 'I' and resid 862 through 875 removed outlier: 3.973A pdb=" N LEU I 875 " --> pdb=" O THR I 871 " (cutoff:3.500A) Processing helix chain 'I' and resid 880 through 885 removed outlier: 4.061A pdb=" N ILE I 884 " --> pdb=" O VAL I 880 " (cutoff:3.500A) Processing helix chain 'I' and resid 889 through 898 Processing helix chain 'I' and resid 921 through 930 removed outlier: 4.206A pdb=" N LYS I 925 " --> pdb=" O ILE I 921 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE I 930 " --> pdb=" O THR I 926 " (cutoff:3.500A) Processing helix chain 'I' and resid 933 through 938 Processing helix chain 'I' and resid 938 through 948 removed outlier: 3.896A pdb=" N LEU I 944 " --> pdb=" O LEU I 940 " (cutoff:3.500A) Processing helix chain 'I' and resid 957 through 962 Processing helix chain 'J' and resid 266 through 288 removed outlier: 3.523A pdb=" N ARG J 288 " --> pdb=" O LEU J 284 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 293 removed outlier: 3.787A pdb=" N ALA J 292 " --> pdb=" O TYR J 289 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU J 293 " --> pdb=" O VAL J 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 289 through 293' Processing helix chain 'J' and resid 307 through 327 Processing helix chain 'J' and resid 380 through 397 removed outlier: 4.264A pdb=" N ALA J 384 " --> pdb=" O ILE J 380 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET J 385 " --> pdb=" O SER J 381 " (cutoff:3.500A) Proline residue: J 388 - end of helix Processing helix chain 'J' and resid 402 through 417 Proline residue: J 410 - end of helix Processing helix chain 'J' and resid 426 through 442 Proline residue: J 436 - end of helix removed outlier: 4.117A pdb=" N VAL J 439 " --> pdb=" O ALA J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 476 removed outlier: 4.530A pdb=" N LEU J 465 " --> pdb=" O SER J 461 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN J 467 " --> pdb=" O ASP J 463 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU J 476 " --> pdb=" O GLN J 472 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 495 removed outlier: 3.781A pdb=" N TYR J 491 " --> pdb=" O ARG J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 506 through 525 Processing helix chain 'J' and resid 526 through 543 Processing helix chain 'J' and resid 551 through 565 removed outlier: 3.714A pdb=" N ARG J 555 " --> pdb=" O HIS J 551 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU J 565 " --> pdb=" O ILE J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 585 through 602 removed outlier: 3.988A pdb=" N LEU J 594 " --> pdb=" O LYS J 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS J 597 " --> pdb=" O GLN J 593 " (cutoff:3.500A) Processing helix chain 'J' and resid 604 through 616 removed outlier: 3.744A pdb=" N VAL J 608 " --> pdb=" O ASP J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 617 through 619 No H-bonds generated for 'chain 'J' and resid 617 through 619' Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.855A pdb=" N LEU J 631 " --> pdb=" O GLU J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 641 Processing helix chain 'J' and resid 897 through 909 Proline residue: J 903 - end of helix Processing helix chain 'J' and resid 1016 through 1028 removed outlier: 3.811A pdb=" N GLU J1020 " --> pdb=" O VAL J1016 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR J1021 " --> pdb=" O ASP J1017 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA J1028 " --> pdb=" O SER J1024 " (cutoff:3.500A) Processing helix chain 'J' and resid 1110 through 1129 removed outlier: 3.648A pdb=" N THR J1114 " --> pdb=" O ASN J1110 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG J1124 " --> pdb=" O LYS J1120 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER J1129 " --> pdb=" O GLU J1125 " (cutoff:3.500A) Processing helix chain 'J' and resid 1157 through 1165 removed outlier: 3.519A pdb=" N VAL J1161 " --> pdb=" O ASP J1157 " (cutoff:3.500A) Processing helix chain 'J' and resid 1166 through 1169 Processing helix chain 'K' and resid 237 through 249 removed outlier: 4.080A pdb=" N PHE K 247 " --> pdb=" O LEU K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 483 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.725A pdb=" N LEU A 19 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 7 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 84 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AA3, first strand: chain 'C' and resid 104 through 106 removed outlier: 3.717A pdb=" N PHE C 115 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 178 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 176 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 160 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.660A pdb=" N VAL B 96 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 175 through 178 removed outlier: 3.640A pdb=" N ASN B 175 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 184 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 262 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B 260 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.761A pdb=" N PHE D 17 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER D 5 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 91 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP D 7 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 89 " --> pdb=" O TRP D 7 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ARG D 68 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE D 67 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR E 124 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 69 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU E 122 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER D 71 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG E 120 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'F' and resid 104 through 106 removed outlier: 3.558A pdb=" N ASN F 104 " --> pdb=" O ILE F 118 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR F 174 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU F 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL F 164 " --> pdb=" O GLU F 175 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP F 162 " --> pdb=" O LYS F 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS F 179 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP F 158 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 34 through 36 removed outlier: 3.644A pdb=" N THR H 21 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR H 16 " --> pdb=" O ILE H 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 198 through 201 removed outlier: 3.690A pdb=" N TYR G 209 " --> pdb=" O ILE G 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 88 through 94 removed outlier: 5.389A pdb=" N GLY H 90 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA H 102 " --> pdb=" O GLY H 90 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE H 100 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 562 through 565 Processing sheet with id=AB4, first strand: chain 'I' and resid 593 through 594 removed outlier: 4.009A pdb=" N VAL I 593 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE I 609 " --> pdb=" O VAL I 593 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 674 through 675 removed outlier: 3.542A pdb=" N GLU I 728 " --> pdb=" O VAL I 689 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 722 through 723 Processing sheet with id=AB7, first strand: chain 'I' and resid 769 through 777 Processing sheet with id=AB8, first strand: chain 'I' and resid 819 through 820 removed outlier: 3.610A pdb=" N TYR I 819 " --> pdb=" O SER I 802 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU I 799 " --> pdb=" O ASN I 860 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN I 860 " --> pdb=" O LEU I 799 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER I 801 " --> pdb=" O ARG I 858 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN I 854 " --> pdb=" O SER I 805 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 988 through 992 removed outlier: 3.700A pdb=" N ASP I1031 " --> pdb=" O GLN I 992 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 1014 through 1016 removed outlier: 6.812A pdb=" N THR I1014 " --> pdb=" O GLU I1062 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU I1062 " --> pdb=" O THR I1014 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 772 through 773 removed outlier: 4.634A pdb=" N ASP J 751 " --> pdb=" O VAL J 773 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER J 755 " --> pdb=" O SER J 804 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER J 804 " --> pdb=" O SER J 755 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 860 through 861 Processing sheet with id=AC4, first strand: chain 'J' and resid 929 through 930 removed outlier: 6.805A pdb=" N ARG J 930 " --> pdb=" O MET J 970 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 1000 through 1004 removed outlier: 3.861A pdb=" N LEU J1042 " --> pdb=" O ILE J1076 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE J1044 " --> pdb=" O SER J1074 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 1134 through 1135 Processing sheet with id=AC7, first strand: chain 'J' and resid 1171 through 1177 removed outlier: 3.750A pdb=" N GLN J1174 " --> pdb=" O ILE J1193 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 1181 through 1182 removed outlier: 3.703A pdb=" N TYR J1261 " --> pdb=" O LEU J1286 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU J1262 " --> pdb=" O PHE J1216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE J1216 " --> pdb=" O GLU J1262 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER J1264 " --> pdb=" O VAL J1214 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL J1214 " --> pdb=" O SER J1264 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 215 through 223 removed outlier: 3.732A pdb=" N LYS K 223 " --> pdb=" O CYS K 227 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS K 227 " --> pdb=" O LYS K 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 284 through 285 removed outlier: 3.872A pdb=" N VAL K 285 " --> pdb=" O LYS K 258 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS K 258 " --> pdb=" O VAL K 285 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 306 through 311 Processing sheet with id=AD3, first strand: chain 'K' and resid 403 through 404 removed outlier: 3.645A pdb=" N PHE K 427 " --> pdb=" O PHE K 524 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE K 524 " --> pdb=" O PHE K 427 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA K 520 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 419 through 421 removed outlier: 6.114A pdb=" N LYS K 420 " --> pdb=" O VAL K 557 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER K 556 " --> pdb=" O TYR K 532 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 507 through 508 removed outlier: 3.836A pdb=" N GLU K 547 " --> pdb=" O ASP K 542 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2739 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: 8.04 Time building geometry restraints manager: 9.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6724 1.34 - 1.46: 5271 1.46 - 1.58: 11558 1.58 - 1.71: 1 1.71 - 1.83: 138 Bond restraints: 23692 Sorted by residual: bond pdb=" C GLY J 769 " pdb=" N PRO J 770 " ideal model delta sigma weight residual 1.334 1.377 -0.044 8.40e-03 1.42e+04 2.73e+01 bond pdb=" N GLN E 56 " pdb=" CA GLN E 56 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.15e+01 bond pdb=" CA ARG F 169 " pdb=" C ARG F 169 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.56e-02 4.11e+03 1.32e+01 bond pdb=" N MET J 909 " pdb=" CA MET J 909 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.69e+00 bond pdb=" N ILE J1215 " pdb=" CA ILE J1215 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.19e-02 7.06e+03 9.41e+00 ... (remaining 23687 not shown) Histogram of bond angle deviations from ideal: 86.99 - 96.96: 4 96.96 - 106.93: 572 106.93 - 116.90: 15873 116.90 - 126.87: 15502 126.87 - 136.84: 284 Bond angle restraints: 32235 Sorted by residual: angle pdb=" N VAL F 155 " pdb=" CA VAL F 155 " pdb=" C VAL F 155 " ideal model delta sigma weight residual 112.17 103.15 9.02 9.50e-01 1.11e+00 9.02e+01 angle pdb=" N PRO I 639 " pdb=" CA PRO I 639 " pdb=" CB PRO I 639 " ideal model delta sigma weight residual 103.25 112.01 -8.76 1.05e+00 9.07e-01 6.95e+01 angle pdb=" N PRO I 346 " pdb=" CA PRO I 346 " pdb=" CB PRO I 346 " ideal model delta sigma weight residual 103.25 111.92 -8.67 1.05e+00 9.07e-01 6.82e+01 angle pdb=" N PRO I 483 " pdb=" CA PRO I 483 " pdb=" CB PRO I 483 " ideal model delta sigma weight residual 103.25 111.89 -8.64 1.05e+00 9.07e-01 6.77e+01 angle pdb=" N PRO K 310 " pdb=" CA PRO K 310 " pdb=" CB PRO K 310 " ideal model delta sigma weight residual 103.25 111.70 -8.45 1.05e+00 9.07e-01 6.47e+01 ... (remaining 32230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 13011 18.12 - 36.24: 1026 36.24 - 54.35: 148 54.35 - 72.47: 42 72.47 - 90.59: 18 Dihedral angle restraints: 14245 sinusoidal: 4550 harmonic: 9695 Sorted by residual: dihedral pdb=" CA TYR J 648 " pdb=" C TYR J 648 " pdb=" N TRP J 649 " pdb=" CA TRP J 649 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR I 995 " pdb=" C THR I 995 " pdb=" N SER I 996 " pdb=" CA SER I 996 " ideal model delta harmonic sigma weight residual 180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR K 545 " pdb=" C THR K 545 " pdb=" N ASN K 546 " pdb=" CA ASN K 546 " ideal model delta harmonic sigma weight residual -180.00 -152.42 -27.58 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 14242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3261 0.099 - 0.198: 467 0.198 - 0.297: 85 0.297 - 0.396: 19 0.396 - 0.495: 4 Chirality restraints: 3836 Sorted by residual: chirality pdb=" CB THR G 219 " pdb=" CA THR G 219 " pdb=" OG1 THR G 219 " pdb=" CG2 THR G 219 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CB ILE J 760 " pdb=" CA ILE J 760 " pdb=" CG1 ILE J 760 " pdb=" CG2 ILE J 760 " both_signs ideal model delta sigma weight residual False 2.64 3.09 -0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CB ILE F 143 " pdb=" CA ILE F 143 " pdb=" CG1 ILE F 143 " pdb=" CG2 ILE F 143 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 3833 not shown) Planarity restraints: 4197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 212 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 213 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 162 " 0.037 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP C 162 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP C 162 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 162 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 162 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 162 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 162 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 162 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 162 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 162 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 172 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C ARG G 172 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG G 172 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP G 173 " 0.021 2.00e-02 2.50e+03 ... (remaining 4194 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 10 2.23 - 2.90: 8749 2.90 - 3.57: 32284 3.57 - 4.23: 48424 4.23 - 4.90: 81176 Nonbonded interactions: 170643 Sorted by model distance: nonbonded pdb=" CZ3 TRP J 906 " pdb=" O ILE J1095 " model vdw 1.563 3.340 nonbonded pdb=" CE3 TRP J 906 " pdb=" O ILE J1095 " model vdw 1.741 3.340 nonbonded pdb=" NH1 ARG D 19 " pdb=" O ALA D 24 " model vdw 2.017 2.520 nonbonded pdb=" OH TYR D 4 " pdb=" OD2 ASP D 93 " model vdw 2.030 2.440 nonbonded pdb=" OD2 ASP J 478 " pdb=" CE1 PHE J 488 " model vdw 2.070 3.340 ... (remaining 170638 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 'C' and resid 8 through 189) 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=0.00 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: 7.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 22.810 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 60.420 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 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 : 0.007 0.079 23692 Z= 0.449 Angle : 1.440 23.705 32235 Z= 0.806 Chirality : 0.076 0.495 3836 Planarity : 0.008 0.103 4197 Dihedral : 14.416 90.588 7909 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.99 % Favored : 89.14 % Rotamer: Outliers : 0.69 % Allowed : 1.19 % Favored : 98.12 % Cbeta Deviations : 0.09 % 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: -4.65 (0.11), residues: 3233 helix: -2.69 (0.11), residues: 1083 sheet: -2.44 (0.20), residues: 579 loop : -3.67 (0.12), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP C 162 HIS 0.011 0.002 HIS J1126 PHE 0.047 0.004 PHE H 95 TYR 0.048 0.004 TYR J 905 ARG 0.025 0.002 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 449 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.5126 (tpt) cc_final: 0.4875 (tpt) REVERT: A 75 PHE cc_start: 0.8448 (m-80) cc_final: 0.8079 (m-80) REVERT: C 45 TYR cc_start: 0.4538 (m-10) cc_final: 0.4246 (m-10) REVERT: C 59 MET cc_start: 0.8305 (tpp) cc_final: 0.7917 (tpp) REVERT: B 140 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: B 187 LEU cc_start: 0.7020 (tp) cc_final: 0.6785 (tp) REVERT: D 35 LYS cc_start: 0.6916 (pttm) cc_final: 0.6594 (pttm) REVERT: D 139 LYS cc_start: 0.7292 (tmtt) cc_final: 0.6891 (mttp) REVERT: D 141 THR cc_start: 0.6694 (t) cc_final: 0.6170 (t) REVERT: E 132 TYR cc_start: 0.6000 (t80) cc_final: 0.5377 (t80) REVERT: G 169 MET cc_start: 0.7519 (mmp) cc_final: 0.6797 (mmm) REVERT: H 40 ILE cc_start: 0.8813 (pt) cc_final: 0.8581 (pt) REVERT: H 113 MET cc_start: 0.8143 (tmm) cc_final: 0.7781 (tmm) REVERT: J 519 GLU cc_start: 0.6271 (tt0) cc_final: 0.6042 (tt0) REVERT: J 651 PRO cc_start: 0.8976 (Cg_endo) cc_final: 0.8729 (Cg_exo) REVERT: J 739 PHE cc_start: 0.6614 (t80) cc_final: 0.6360 (t80) REVERT: J 808 LEU cc_start: 0.6431 (pp) cc_final: 0.5826 (tp) REVERT: J 821 ARG cc_start: 0.6144 (ppt170) cc_final: 0.5567 (ptt90) REVERT: J 1041 LEU cc_start: 0.7876 (mt) cc_final: 0.7602 (mp) REVERT: J 1226 ARG cc_start: 0.7879 (pmt-80) cc_final: 0.7474 (pmt-80) REVERT: K 550 GLU cc_start: 0.7189 (tp30) cc_final: 0.6817 (tm-30) outliers start: 14 outliers final: 2 residues processed: 458 average time/residue: 0.3671 time to fit residues: 254.3625 Evaluate side-chains 258 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 255 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain J residue 907 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 274 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 295 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 24 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 94 HIS B 143 ASN B 180 HIS ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 625 GLN ** K 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 485 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 23692 Z= 0.456 Angle : 0.851 9.336 32235 Z= 0.459 Chirality : 0.050 0.254 3836 Planarity : 0.006 0.065 4197 Dihedral : 6.944 51.015 3461 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.74 % Favored : 87.07 % Rotamer: Outliers : 3.22 % Allowed : 13.56 % Favored : 83.23 % 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: -3.49 (0.13), residues: 3233 helix: -0.60 (0.15), residues: 1092 sheet: -2.35 (0.20), residues: 609 loop : -3.69 (0.13), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP J 649 HIS 0.009 0.002 HIS I 997 PHE 0.033 0.003 PHE I 829 TYR 0.051 0.003 TYR H 96 ARG 0.007 0.001 ARG K 430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 248 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 GLU cc_start: 0.6028 (pt0) cc_final: 0.5699 (pt0) REVERT: D 67 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8946 (mp) REVERT: H 113 MET cc_start: 0.8036 (tmm) cc_final: 0.7715 (tmm) REVERT: J 643 GLU cc_start: 0.8216 (pm20) cc_final: 0.7999 (pm20) REVERT: J 821 ARG cc_start: 0.6119 (ppt170) cc_final: 0.5602 (ptt90) REVERT: J 907 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7265 (mmtm) REVERT: K 415 ILE cc_start: 0.8020 (mt) cc_final: 0.7754 (mt) outliers start: 65 outliers final: 40 residues processed: 293 average time/residue: 0.3145 time to fit residues: 150.1304 Evaluate side-chains 260 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 CYS Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 806 LEU Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1082 LYS Chi-restraints excluded: chain J residue 1140 ASP Chi-restraints excluded: chain J residue 1211 LEU Chi-restraints excluded: chain J residue 1212 ASP Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 489 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 164 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 319 optimal weight: 2.9990 chunk 263 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23692 Z= 0.222 Angle : 0.675 9.828 32235 Z= 0.355 Chirality : 0.045 0.181 3836 Planarity : 0.004 0.057 4197 Dihedral : 6.001 39.733 3459 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.95 % Favored : 88.80 % Rotamer: Outliers : 2.67 % Allowed : 17.81 % Favored : 79.52 % 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: -2.91 (0.14), residues: 3233 helix: 0.19 (0.16), residues: 1106 sheet: -2.12 (0.21), residues: 607 loop : -3.61 (0.13), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 649 HIS 0.005 0.001 HIS G 92 PHE 0.034 0.002 PHE H 95 TYR 0.044 0.002 TYR H 96 ARG 0.007 0.001 ARG K 430 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 247 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 12 HIS cc_start: 0.6163 (m-70) cc_final: 0.5727 (m170) REVERT: D 66 ASP cc_start: 0.8443 (m-30) cc_final: 0.8119 (m-30) REVERT: J 538 MET cc_start: 0.8404 (mtp) cc_final: 0.8150 (mtp) REVERT: J 821 ARG cc_start: 0.6046 (ppt170) cc_final: 0.5555 (ptt90) REVERT: J 907 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7651 (mptt) outliers start: 54 outliers final: 31 residues processed: 287 average time/residue: 0.3147 time to fit residues: 148.0883 Evaluate side-chains 249 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 217 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 CYS Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1022 VAL Chi-restraints excluded: chain J residue 1173 VAL Chi-restraints excluded: chain J residue 1212 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 292 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN D 56 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 HIS H 120 ASN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 625 GLN ** K 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23692 Z= 0.248 Angle : 0.669 14.173 32235 Z= 0.351 Chirality : 0.045 0.457 3836 Planarity : 0.004 0.056 4197 Dihedral : 5.761 48.151 3457 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.91 % Favored : 87.84 % Rotamer: Outliers : 3.41 % Allowed : 20.44 % Favored : 76.15 % 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: -2.66 (0.14), residues: 3233 helix: 0.54 (0.16), residues: 1103 sheet: -2.10 (0.21), residues: 609 loop : -3.52 (0.13), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 649 HIS 0.004 0.001 HIS I 997 PHE 0.027 0.002 PHE F 49 TYR 0.034 0.002 TYR H 96 ARG 0.007 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 227 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 66 ASP cc_start: 0.8430 (m-30) cc_final: 0.8100 (m-30) REVERT: F 115 PHE cc_start: 0.8248 (p90) cc_final: 0.8018 (p90) REVERT: G 192 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: H 103 TYR cc_start: 0.6504 (t80) cc_final: 0.6265 (t80) REVERT: J 821 ARG cc_start: 0.6077 (ppt170) cc_final: 0.5588 (ptt90) REVERT: J 907 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7573 (mmtm) outliers start: 69 outliers final: 42 residues processed: 282 average time/residue: 0.3087 time to fit residues: 144.4750 Evaluate side-chains 264 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 220 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 TRP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 192 PHE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 905 TYR Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1009 PHE Chi-restraints excluded: chain J residue 1022 VAL Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1173 VAL Chi-restraints excluded: chain J residue 1211 LEU Chi-restraints excluded: chain J residue 1212 ASP Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 486 GLN Chi-restraints excluded: chain K residue 496 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 261 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 268 optimal weight: 10.0000 chunk 217 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 281 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 HIS ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 749 GLN ** K 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23692 Z= 0.255 Angle : 0.660 14.889 32235 Z= 0.348 Chirality : 0.045 0.382 3836 Planarity : 0.004 0.058 4197 Dihedral : 5.653 50.838 3457 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.66 % Favored : 88.09 % Rotamer: Outliers : 3.61 % Allowed : 22.22 % Favored : 74.17 % 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: -2.55 (0.15), residues: 3233 helix: 0.69 (0.16), residues: 1107 sheet: -2.03 (0.21), residues: 610 loop : -3.53 (0.13), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 649 HIS 0.005 0.001 HIS I 997 PHE 0.024 0.002 PHE F 49 TYR 0.026 0.002 TYR J 619 ARG 0.007 0.001 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 230 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 66 ASP cc_start: 0.8364 (m-30) cc_final: 0.8024 (m-30) REVERT: F 115 PHE cc_start: 0.8276 (p90) cc_final: 0.8012 (p90) REVERT: G 192 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: H 103 TYR cc_start: 0.6572 (t80) cc_final: 0.6278 (t80) REVERT: H 109 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7764 (mmt) REVERT: J 821 ARG cc_start: 0.6088 (ppt170) cc_final: 0.5604 (ptt90) REVERT: J 907 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7734 (mmtm) REVERT: J 1125 GLU cc_start: 0.7115 (tt0) cc_final: 0.6768 (tm-30) REVERT: K 484 GLU cc_start: 0.7811 (pm20) cc_final: 0.7598 (pm20) outliers start: 73 outliers final: 46 residues processed: 285 average time/residue: 0.2985 time to fit residues: 141.2108 Evaluate side-chains 267 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 218 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 TRP Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 192 PHE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 519 GLU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1009 PHE Chi-restraints excluded: chain J residue 1022 VAL Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1043 ASP Chi-restraints excluded: chain J residue 1173 VAL Chi-restraints excluded: chain J residue 1211 LEU Chi-restraints excluded: chain J residue 1212 ASP Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 486 GLN Chi-restraints excluded: chain K residue 496 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 105 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 314 optimal weight: 0.0270 chunk 261 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 165 optimal weight: 0.0570 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 HIS ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23692 Z= 0.176 Angle : 0.621 10.826 32235 Z= 0.323 Chirality : 0.044 0.227 3836 Planarity : 0.003 0.058 4197 Dihedral : 5.249 47.481 3457 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.27 % Favored : 89.48 % Rotamer: Outliers : 3.17 % Allowed : 23.21 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.15), residues: 3233 helix: 1.00 (0.16), residues: 1105 sheet: -1.87 (0.22), residues: 608 loop : -3.41 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 649 HIS 0.004 0.001 HIS G 92 PHE 0.025 0.001 PHE C 30 TYR 0.025 0.001 TYR H 96 ARG 0.007 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 246 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8261 (m-80) cc_final: 0.7927 (m-80) REVERT: D 12 HIS cc_start: 0.6322 (m-70) cc_final: 0.5627 (m170) REVERT: D 22 THR cc_start: 0.7166 (OUTLIER) cc_final: 0.6964 (p) REVERT: D 66 ASP cc_start: 0.8244 (m-30) cc_final: 0.7942 (m-30) REVERT: G 192 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: H 103 TYR cc_start: 0.6723 (t80) cc_final: 0.6425 (t80) REVERT: J 821 ARG cc_start: 0.6081 (ppt170) cc_final: 0.5620 (ptt90) REVERT: J 907 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7795 (mmtm) REVERT: J 1125 GLU cc_start: 0.7043 (tt0) cc_final: 0.6805 (tm-30) outliers start: 64 outliers final: 36 residues processed: 294 average time/residue: 0.3012 time to fit residues: 146.5816 Evaluate side-chains 267 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 228 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 192 PHE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 836 ILE Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 905 TYR Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1009 PHE Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1173 VAL Chi-restraints excluded: chain J residue 1212 ASP Chi-restraints excluded: chain J residue 1274 ASP Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 303 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 177 optimal weight: 0.0670 chunk 264 optimal weight: 0.0980 chunk 175 optimal weight: 20.0000 chunk 313 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 190 optimal weight: 0.3980 chunk 144 optimal weight: 20.0000 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 HIS ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 409 ASN ** K 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 0.045 23692 Z= 0.188 Angle : 0.637 12.559 32235 Z= 0.329 Chirality : 0.044 0.209 3836 Planarity : 0.004 0.066 4197 Dihedral : 5.139 49.413 3457 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.33 % Favored : 89.39 % Rotamer: Outliers : 2.92 % Allowed : 24.00 % Favored : 73.08 % 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: -2.11 (0.15), residues: 3233 helix: 1.15 (0.16), residues: 1100 sheet: -1.79 (0.22), residues: 606 loop : -3.33 (0.14), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 649 HIS 0.004 0.001 HIS D 12 PHE 0.022 0.001 PHE F 49 TYR 0.025 0.001 TYR J 491 ARG 0.004 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 243 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8246 (m-80) cc_final: 0.7944 (m-80) REVERT: D 22 THR cc_start: 0.7084 (OUTLIER) cc_final: 0.6855 (p) REVERT: D 66 ASP cc_start: 0.8262 (m-30) cc_final: 0.7945 (m-30) REVERT: G 192 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: H 103 TYR cc_start: 0.6707 (t80) cc_final: 0.6395 (t80) REVERT: H 109 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7626 (mmt) REVERT: J 821 ARG cc_start: 0.6100 (ppt170) cc_final: 0.5637 (ptt90) REVERT: J 907 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7814 (mmtm) REVERT: K 484 GLU cc_start: 0.7752 (pm20) cc_final: 0.7485 (pm20) outliers start: 59 outliers final: 37 residues processed: 290 average time/residue: 0.3257 time to fit residues: 154.2687 Evaluate side-chains 267 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 226 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 TRP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 192 PHE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 542 LEU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 905 TYR Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1009 PHE Chi-restraints excluded: chain J residue 1022 VAL Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1043 ASP Chi-restraints excluded: chain J residue 1173 VAL Chi-restraints excluded: chain J residue 1212 ASP Chi-restraints excluded: chain J residue 1274 ASP Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 193 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN D 101 GLN D 104 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 409 ASN ** K 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 0.049 23692 Z= 0.222 Angle : 0.649 11.010 32235 Z= 0.337 Chirality : 0.044 0.165 3836 Planarity : 0.004 0.063 4197 Dihedral : 5.227 53.673 3457 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.17 % Favored : 88.56 % Rotamer: Outliers : 3.07 % Allowed : 24.69 % Favored : 72.24 % 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: -2.07 (0.15), residues: 3233 helix: 1.21 (0.16), residues: 1100 sheet: -1.80 (0.22), residues: 610 loop : -3.30 (0.14), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 649 HIS 0.004 0.001 HIS I 997 PHE 0.017 0.001 PHE F 49 TYR 0.026 0.002 TYR J 619 ARG 0.004 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 225 time to evaluate : 2.384 Fit side-chains REVERT: A 75 PHE cc_start: 0.8290 (m-80) cc_final: 0.7971 (m-80) REVERT: D 22 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6865 (p) REVERT: D 66 ASP cc_start: 0.8250 (m-30) cc_final: 0.7925 (m-30) REVERT: G 192 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: H 103 TYR cc_start: 0.6620 (t80) cc_final: 0.6354 (t80) REVERT: H 109 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7636 (mmt) REVERT: J 538 MET cc_start: 0.8481 (mtp) cc_final: 0.8242 (mtp) REVERT: J 821 ARG cc_start: 0.6098 (ppt170) cc_final: 0.5639 (ptt90) REVERT: J 907 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7801 (mmtm) outliers start: 62 outliers final: 46 residues processed: 272 average time/residue: 0.3055 time to fit residues: 137.5093 Evaluate side-chains 266 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 216 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 TRP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 108 TRP Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 192 PHE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 836 ILE Chi-restraints excluded: chain J residue 519 GLU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 905 TYR Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1001 ASP Chi-restraints excluded: chain J residue 1013 VAL Chi-restraints excluded: chain J residue 1022 VAL Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1043 ASP Chi-restraints excluded: chain J residue 1080 ILE Chi-restraints excluded: chain J residue 1173 VAL Chi-restraints excluded: chain J residue 1212 ASP Chi-restraints excluded: chain J residue 1274 ASP Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 284 optimal weight: 0.6980 chunk 300 optimal weight: 6.9990 chunk 273 optimal weight: 0.8980 chunk 291 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 276 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 HIS ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23692 Z= 0.209 Angle : 0.658 14.865 32235 Z= 0.338 Chirality : 0.044 0.337 3836 Planarity : 0.004 0.067 4197 Dihedral : 5.165 52.698 3457 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.95 % Favored : 88.80 % Rotamer: Outliers : 2.77 % Allowed : 25.19 % Favored : 72.04 % 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: -2.04 (0.15), residues: 3233 helix: 1.21 (0.16), residues: 1102 sheet: -1.75 (0.22), residues: 611 loop : -3.29 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 649 HIS 0.008 0.001 HIS D 12 PHE 0.019 0.001 PHE F 49 TYR 0.026 0.001 TYR H 96 ARG 0.004 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 221 time to evaluate : 3.039 Fit side-chains revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8337 (m-80) cc_final: 0.8004 (m-80) REVERT: D 22 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6839 (p) REVERT: D 66 ASP cc_start: 0.8240 (m-30) cc_final: 0.7909 (m-30) REVERT: G 192 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: H 103 TYR cc_start: 0.6584 (t80) cc_final: 0.6334 (t80) REVERT: H 109 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7651 (mmt) REVERT: J 821 ARG cc_start: 0.6175 (ppt170) cc_final: 0.5717 (ptt90) REVERT: J 907 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7849 (mmtm) outliers start: 56 outliers final: 48 residues processed: 264 average time/residue: 0.3104 time to fit residues: 137.3418 Evaluate side-chains 266 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 214 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 TRP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 108 TRP Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 192 PHE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 836 ILE Chi-restraints excluded: chain J residue 519 GLU Chi-restraints excluded: chain J residue 542 LEU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 905 TYR Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1001 ASP Chi-restraints excluded: chain J residue 1013 VAL Chi-restraints excluded: chain J residue 1022 VAL Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1043 ASP Chi-restraints excluded: chain J residue 1080 ILE Chi-restraints excluded: chain J residue 1173 VAL Chi-restraints excluded: chain J residue 1194 THR Chi-restraints excluded: chain J residue 1212 ASP Chi-restraints excluded: chain J residue 1274 ASP Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 191 optimal weight: 0.0070 chunk 308 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 323 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 158 optimal weight: 0.0000 overall best weight: 1.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1209 ASN ** K 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23692 Z= 0.331 Angle : 0.738 16.362 32235 Z= 0.384 Chirality : 0.046 0.194 3836 Planarity : 0.004 0.066 4197 Dihedral : 5.656 53.676 3457 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.11 % Favored : 86.64 % Rotamer: Outliers : 2.82 % Allowed : 25.38 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 3233 helix: 0.97 (0.16), residues: 1105 sheet: -1.91 (0.21), residues: 604 loop : -3.46 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 649 HIS 0.006 0.001 HIS I 997 PHE 0.023 0.002 PHE J1037 TYR 0.027 0.002 TYR H 96 ARG 0.006 0.001 ARG B 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 211 time to evaluate : 2.752 Fit side-chains REVERT: D 22 THR cc_start: 0.7337 (OUTLIER) cc_final: 0.6889 (p) REVERT: D 66 ASP cc_start: 0.8350 (m-30) cc_final: 0.8045 (m-30) REVERT: G 192 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: H 109 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7974 (mmt) REVERT: J 821 ARG cc_start: 0.6256 (ppt170) cc_final: 0.5936 (ppt170) REVERT: J 907 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7781 (mmtm) outliers start: 57 outliers final: 47 residues processed: 255 average time/residue: 0.3067 time to fit residues: 130.2379 Evaluate side-chains 258 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 207 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 162 TRP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 108 TRP Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 192 PHE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 519 GLU Chi-restraints excluded: chain J residue 542 LEU Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 905 TYR Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1001 ASP Chi-restraints excluded: chain J residue 1022 VAL Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1043 ASP Chi-restraints excluded: chain J residue 1080 ILE Chi-restraints excluded: chain J residue 1173 VAL Chi-restraints excluded: chain J residue 1194 THR Chi-restraints excluded: chain J residue 1212 ASP Chi-restraints excluded: chain J residue 1274 ASP Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 204 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 237 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 108 optimal weight: 0.0970 chunk 265 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.078691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.068940 restraints weight = 137194.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.070034 restraints weight = 86449.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.070490 restraints weight = 62528.073| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23692 Z= 0.217 Angle : 0.685 15.263 32235 Z= 0.350 Chirality : 0.045 0.398 3836 Planarity : 0.004 0.067 4197 Dihedral : 5.343 50.859 3457 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.01 % Favored : 88.74 % Rotamer: Outliers : 2.62 % Allowed : 26.08 % Favored : 71.30 % 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: -2.14 (0.15), residues: 3233 helix: 1.13 (0.16), residues: 1107 sheet: -1.79 (0.22), residues: 604 loop : -3.37 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J 649 HIS 0.004 0.001 HIS K 490 PHE 0.017 0.001 PHE F 49 TYR 0.026 0.002 TYR H 103 ARG 0.004 0.000 ARG B 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4311.06 seconds wall clock time: 79 minutes 10.85 seconds (4750.85 seconds total)