Starting phenix.real_space_refine on Wed Mar 20 18:10:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t30_25647/03_2024/7t30_25647_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t30_25647/03_2024/7t30_25647.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t30_25647/03_2024/7t30_25647_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t30_25647/03_2024/7t30_25647_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t30_25647/03_2024/7t30_25647_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t30_25647/03_2024/7t30_25647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t30_25647/03_2024/7t30_25647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t30_25647/03_2024/7t30_25647_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t30_25647/03_2024/7t30_25647_updated.pdb" } resolution = 3.0 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= 0.005 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 58 7.16 5 Ni 2 6.56 5 P 6 5.49 5 S 260 5.16 5 C 17794 2.51 5 N 4810 2.21 5 O 5196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A ARG 688": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F ARG 218": "NH1" <-> "NH2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F ARG 277": "NH1" <-> "NH2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F ARG 292": "NH1" <-> "NH2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "F ARG 354": "NH1" <-> "NH2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "F ARG 431": "NH1" <-> "NH2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "F ARG 485": "NH1" <-> "NH2" Residue "F GLU 496": "OE1" <-> "OE2" Residue "F GLU 520": "OE1" <-> "OE2" Residue "F GLU 537": "OE1" <-> "OE2" Residue "F ARG 555": "NH1" <-> "NH2" Residue "F GLU 561": "OE1" <-> "OE2" Residue "F GLU 568": "OE1" <-> "OE2" Residue "F ARG 569": "NH1" <-> "NH2" Residue "F ARG 570": "NH1" <-> "NH2" Residue "F GLU 583": "OE1" <-> "OE2" Residue "F GLU 584": "OE1" <-> "OE2" Residue "F GLU 585": "OE1" <-> "OE2" Residue "F ARG 606": "NH1" <-> "NH2" Residue "F GLU 647": "OE1" <-> "OE2" Residue "F GLU 670": "OE1" <-> "OE2" Residue "F GLU 675": "OE1" <-> "OE2" Residue "F GLU 676": "OE1" <-> "OE2" Residue "F GLU 686": "OE1" <-> "OE2" Residue "F ARG 688": "NH1" <-> "NH2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G ARG 167": "NH1" <-> "NH2" Residue "G GLU 179": "OE1" <-> "OE2" Residue "G TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G GLU 231": "OE1" <-> "OE2" Residue "G GLU 239": "OE1" <-> "OE2" Residue "G GLU 256": "OE1" <-> "OE2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G GLU 295": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G GLU 324": "OE1" <-> "OE2" Residue "G GLU 407": "OE1" <-> "OE2" Residue "G GLU 416": "OE1" <-> "OE2" Residue "G GLU 448": "OE1" <-> "OE2" Residue "G GLU 490": "OE1" <-> "OE2" Residue "G ARG 519": "NH1" <-> "NH2" Residue "G GLU 521": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I GLU 33": "OE1" <-> "OE2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "I GLU 193": "OE1" <-> "OE2" Residue "I GLU 200": "OE1" <-> "OE2" Residue "I GLU 211": "OE1" <-> "OE2" Residue "I GLU 214": "OE1" <-> "OE2" Residue "I GLU 215": "OE1" <-> "OE2" Residue "I GLU 236": "OE1" <-> "OE2" Residue "I GLU 241": "OE1" <-> "OE2" Residue "I ARG 248": "NH1" <-> "NH2" Residue "I ARG 250": "NH1" <-> "NH2" Residue "I GLU 269": "OE1" <-> "OE2" Residue "I GLU 307": "OE1" <-> "OE2" Residue "I PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 337": "OE1" <-> "OE2" Residue "I GLU 343": "OE1" <-> "OE2" Residue "I GLU 346": "OE1" <-> "OE2" Residue "I ARG 360": "NH1" <-> "NH2" Residue "I GLU 375": "OE1" <-> "OE2" Residue "I GLU 389": "OE1" <-> "OE2" Residue "I GLU 414": "OE1" <-> "OE2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "J GLU 174": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28126 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5183 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 34, 'TRANS': 631} Chain breaks: 1 Chain: "B" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3236 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 21, 'TRANS': 403} Chain: "C" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 570 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 66} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3537 Classifications: {'peptide': 447} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 421} Chain: "E" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1398 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 165} Chain: "F" Number of atoms: 5183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5183 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 34, 'TRANS': 631} Chain breaks: 1 Chain: "G" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3236 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 21, 'TRANS': 403} Chain: "H" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 570 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 66} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3537 Classifications: {'peptide': 447} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 421} Chain: "J" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1398 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 165} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'FES': 1, 'FMN': 1, 'NAD': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 7 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {'FCO': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'FES': 1, 'FMN': 1, 'NAD': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 7 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {'FCO': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 270 SG CYS A 36 44.172 101.450 60.058 1.00 46.31 S ATOM 349 SG CYS A 47 41.463 99.544 60.756 1.00 47.94 S ATOM 374 SG CYS A 50 38.470 104.204 59.274 1.00 49.09 S ATOM 477 SG CYS A 64 41.361 105.696 59.031 1.00 50.91 S ATOM 1573 SG CYS A 202 52.155 94.959 67.169 1.00 42.01 S ATOM 1165 SG CYS A 148 52.131 91.909 61.992 1.00 42.98 S ATOM 1212 SG CYS A 154 55.092 96.938 62.834 1.00 46.10 S ATOM 1186 SG CYS A 151 49.591 97.093 63.035 1.00 45.88 S ATOM 1532 SG CYS A 195 63.040 102.435 69.746 1.00 46.45 S ATOM 1244 SG CYS A 158 62.326 101.131 64.631 1.00 48.50 S ATOM 1547 SG CYS A 198 59.731 97.817 68.518 1.00 44.62 S ATOM 1511 SG CYS A 192 66.151 97.515 67.414 1.00 51.71 S ATOM 2033 SG CYS A 264 66.083 106.984 77.365 1.00 48.42 S ATOM 1803 SG CYS A 232 67.591 111.828 78.717 1.00 53.45 S ATOM 1782 SG CYS A 229 63.927 108.887 81.504 1.00 48.62 S ATOM 1825 SG CYS A 236 62.175 111.421 76.713 1.00 50.06 S ATOM 796 SG CYS A 103 48.639 87.797 72.751 1.00 44.41 S ATOM 835 SG CYS A 109 44.976 92.109 70.428 1.00 45.79 S ATOM 770 SG CYS A 100 42.591 85.852 71.893 1.00 44.77 S ATOM 7805 SG CYS B 458 43.662 96.895 50.547 1.00 47.18 S ATOM 8134 SG CYS B 501 44.326 98.500 46.396 1.00 51.48 S ATOM 7825 SG CYS B 461 42.758 92.680 47.348 1.00 47.31 S ATOM 7786 SG CYS B 455 47.636 96.530 47.938 1.00 52.38 S ATOM 7644 SG CYS B 438 31.697 75.778 36.247 1.00 74.16 S ATOM 8377 SG CYS B 531 31.547 72.258 36.169 1.00 80.87 S ATOM 7946 SG CYS B 476 35.835 73.318 39.806 1.00 65.95 S ATOM 8412 SG CYS B 536 35.294 69.607 38.404 1.00 86.69 S ATOM 9494 SG CYS D 64 43.761 67.673 84.790 1.00 37.35 S ATOM 9512 SG CYS D 67 46.129 67.541 87.653 1.00 37.66 S ATOM 12483 SG CYS D 444 43.620 64.597 86.867 1.00 42.69 S ATOM 12503 SG CYS D 447 47.347 66.223 84.816 1.00 39.43 S ATOM 9512 SG CYS D 67 46.129 67.541 87.653 1.00 37.66 S ATOM 12503 SG CYS D 447 47.347 66.223 84.816 1.00 39.43 S ATOM 12649 SG CYS E 17 36.198 74.039 78.339 1.00 43.24 S ATOM 12634 SG CYS E 14 41.773 71.877 79.902 1.00 39.49 S ATOM 13678 SG CYS E 149 41.947 77.464 77.815 1.00 43.23 S ATOM 13186 SG CYS E 85 40.912 73.515 73.869 1.00 43.33 S ATOM 14194 SG CYS F 36 108.180 45.934 60.058 1.00 46.31 S ATOM 14273 SG CYS F 47 110.889 47.840 60.756 1.00 47.94 S ATOM 14298 SG CYS F 50 113.882 43.180 59.274 1.00 49.09 S ATOM 14401 SG CYS F 64 110.991 41.688 59.031 1.00 50.91 S ATOM 15497 SG CYS F 202 100.197 52.425 67.169 1.00 42.01 S ATOM 15089 SG CYS F 148 100.221 55.475 61.992 1.00 42.98 S ATOM 15136 SG CYS F 154 97.260 50.446 62.834 1.00 46.10 S ATOM 15110 SG CYS F 151 102.761 50.291 63.035 1.00 45.88 S ATOM 15456 SG CYS F 195 89.312 44.949 69.746 1.00 46.45 S ATOM 15168 SG CYS F 158 90.026 46.253 64.631 1.00 48.50 S ATOM 15471 SG CYS F 198 92.621 49.567 68.518 1.00 44.62 S ATOM 15435 SG CYS F 192 86.201 49.869 67.414 1.00 51.71 S ATOM 15957 SG CYS F 264 86.269 40.400 77.365 1.00 48.42 S ATOM 15727 SG CYS F 232 84.761 35.556 78.717 1.00 53.45 S ATOM 15706 SG CYS F 229 88.425 38.497 81.504 1.00 48.62 S ATOM 15749 SG CYS F 236 90.177 35.963 76.713 1.00 50.06 S ATOM 14720 SG CYS F 103 103.713 59.587 72.751 1.00 44.41 S ATOM 14759 SG CYS F 109 107.376 55.275 70.428 1.00 45.79 S ATOM 14694 SG CYS F 100 109.761 61.532 71.893 1.00 44.77 S ATOM 21729 SG CYS G 458 108.690 50.489 50.547 1.00 47.18 S ATOM 22058 SG CYS G 501 108.026 48.884 46.396 1.00 51.48 S ATOM 21749 SG CYS G 461 109.594 54.704 47.348 1.00 47.31 S ATOM 21710 SG CYS G 455 104.716 50.854 47.938 1.00 52.38 S ATOM 21568 SG CYS G 438 120.655 71.606 36.247 1.00 74.16 S ATOM 22301 SG CYS G 531 120.805 75.126 36.169 1.00 80.87 S ATOM 21870 SG CYS G 476 116.517 74.066 39.806 1.00 65.95 S ATOM 22336 SG CYS G 536 117.058 77.777 38.404 1.00 86.69 S ATOM 23418 SG CYS I 64 108.591 79.711 84.790 1.00 37.35 S ATOM 23436 SG CYS I 67 106.223 79.843 87.653 1.00 37.66 S ATOM 26407 SG CYS I 444 108.732 82.787 86.867 1.00 42.69 S ATOM 26427 SG CYS I 447 105.005 81.161 84.816 1.00 39.43 S ATOM 23436 SG CYS I 67 106.223 79.843 87.653 1.00 37.66 S ATOM 26427 SG CYS I 447 105.005 81.161 84.816 1.00 39.43 S ATOM 26573 SG CYS J 17 116.154 73.345 78.339 1.00 43.24 S ATOM 26558 SG CYS J 14 110.579 75.507 79.902 1.00 39.49 S ATOM 27602 SG CYS J 149 110.405 69.920 77.815 1.00 43.23 S ATOM 27110 SG CYS J 85 111.440 73.869 73.869 1.00 43.33 S Time building chain proxies: 14.70, per 1000 atoms: 0.52 Number of scatterers: 28126 At special positions: 0 Unit cell: (153.18, 148.212, 125.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ni 2 28.00 Fe 58 26.01 S 260 16.00 P 6 15.00 O 5196 8.00 N 4810 7.00 C 17794 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.87 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 701 " pdb="FE2 FES A 701 " - pdb=" SG CYS A 50 " pdb="FE1 FES A 701 " - pdb=" SG CYS A 36 " pdb="FE2 FES A 701 " - pdb=" SG CYS A 64 " pdb="FE1 FES A 701 " - pdb=" SG CYS A 47 " pdb=" FES B 704 " pdb="FE1 FES B 704 " - pdb=" SG CYS B 531 " pdb="FE2 FES B 704 " - pdb=" SG CYS B 476 " pdb="FE2 FES B 704 " - pdb=" SG CYS B 536 " pdb="FE1 FES B 704 " - pdb=" SG CYS B 438 " pdb="FE1 FES B 704 " - pdb=" NE2 HIS B 525 " pdb=" FES F 701 " pdb="FE2 FES F 701 " - pdb=" SG CYS F 50 " pdb="FE1 FES F 701 " - pdb=" SG CYS F 36 " pdb="FE2 FES F 701 " - pdb=" SG CYS F 64 " pdb="FE1 FES F 701 " - pdb=" SG CYS F 47 " pdb=" FES G 704 " pdb="FE1 FES G 704 " - pdb=" SG CYS G 531 " pdb="FE2 FES G 704 " - pdb=" SG CYS G 476 " pdb="FE2 FES G 704 " - pdb=" SG CYS G 536 " pdb="FE1 FES G 704 " - pdb=" SG CYS G 438 " pdb="FE1 FES G 704 " - pdb=" NE2 HIS G 525 " pdb=" SF4 A 702 " pdb="FE4 SF4 A 702 " - pdb=" SG CYS A 151 " pdb="FE3 SF4 A 702 " - pdb=" SG CYS A 154 " pdb="FE1 SF4 A 702 " - pdb=" SG CYS A 202 " pdb="FE2 SF4 A 702 " - pdb=" SG CYS A 148 " pdb=" SF4 A 703 " pdb="FE2 SF4 A 703 " - pdb=" SG CYS A 158 " pdb="FE1 SF4 A 703 " - pdb=" SG CYS A 195 " pdb="FE4 SF4 A 703 " - pdb=" SG CYS A 192 " pdb="FE3 SF4 A 703 " - pdb=" SG CYS A 198 " pdb=" SF4 A 704 " pdb="FE1 SF4 A 704 " - pdb=" SG CYS A 264 " pdb="FE3 SF4 A 704 " - pdb=" SG CYS A 229 " pdb="FE2 SF4 A 704 " - pdb=" SG CYS A 232 " pdb="FE4 SF4 A 704 " - pdb=" SG CYS A 236 " pdb=" SF4 A 705 " pdb="FE1 SF4 A 705 " - pdb=" SG CYS A 103 " pdb="FE4 SF4 A 705 " - pdb=" SG CYS A 100 " pdb="FE3 SF4 A 705 " - pdb=" SG CYS A 109 " pdb="FE2 SF4 A 705 " - pdb=" ND1 HIS A 98 " pdb=" SF4 B 702 " pdb="FE2 SF4 B 702 " - pdb=" SG CYS B 501 " pdb="FE4 SF4 B 702 " - pdb=" SG CYS B 455 " pdb="FE1 SF4 B 702 " - pdb=" SG CYS B 458 " pdb="FE3 SF4 B 702 " - pdb=" SG CYS B 461 " pdb=" SF4 E 201 " pdb="FE4 SF4 E 201 " - pdb=" SG CYS E 85 " pdb="FE3 SF4 E 201 " - pdb=" SG CYS E 149 " pdb="FE2 SF4 E 201 " - pdb=" SG CYS E 14 " pdb="FE1 SF4 E 201 " - pdb=" SG CYS E 17 " pdb=" SF4 F 702 " pdb="FE4 SF4 F 702 " - pdb=" SG CYS F 151 " pdb="FE3 SF4 F 702 " - pdb=" SG CYS F 154 " pdb="FE1 SF4 F 702 " - pdb=" SG CYS F 202 " pdb="FE2 SF4 F 702 " - pdb=" SG CYS F 148 " pdb=" SF4 F 703 " pdb="FE2 SF4 F 703 " - pdb=" SG CYS F 158 " pdb="FE1 SF4 F 703 " - pdb=" SG CYS F 195 " pdb="FE4 SF4 F 703 " - pdb=" SG CYS F 192 " pdb="FE3 SF4 F 703 " - pdb=" SG CYS F 198 " pdb=" SF4 F 704 " pdb="FE1 SF4 F 704 " - pdb=" SG CYS F 264 " pdb="FE3 SF4 F 704 " - pdb=" SG CYS F 229 " pdb="FE2 SF4 F 704 " - pdb=" SG CYS F 232 " pdb="FE4 SF4 F 704 " - pdb=" SG CYS F 236 " pdb=" SF4 F 705 " pdb="FE1 SF4 F 705 " - pdb=" SG CYS F 103 " pdb="FE4 SF4 F 705 " - pdb=" SG CYS F 100 " pdb="FE3 SF4 F 705 " - pdb=" SG CYS F 109 " pdb="FE2 SF4 F 705 " - pdb=" ND1 HIS F 98 " pdb=" SF4 G 702 " pdb="FE2 SF4 G 702 " - pdb=" SG CYS G 501 " pdb="FE4 SF4 G 702 " - pdb=" SG CYS G 455 " pdb="FE1 SF4 G 702 " - pdb=" SG CYS G 458 " pdb="FE3 SF4 G 702 " - pdb=" SG CYS G 461 " pdb=" SF4 J 201 " pdb="FE4 SF4 J 201 " - pdb=" SG CYS J 85 " pdb="FE3 SF4 J 201 " - pdb=" SG CYS J 149 " pdb="FE2 SF4 J 201 " - pdb=" SG CYS J 14 " pdb="FE1 SF4 J 201 " - pdb=" SG CYS J 17 " Number of angles added : 162 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 22 sheets defined 38.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.39 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.698A pdb=" N ASN A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 95 Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 265 through 274 removed outlier: 4.428A pdb=" N LEU A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.640A pdb=" N ALA A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 350 through 366 Proline residue: A 362 - end of helix removed outlier: 4.972A pdb=" N GLN A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.746A pdb=" N ILE A 377 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 378 " --> pdb=" O HIS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 393 No H-bonds generated for 'chain 'A' and resid 390 through 393' Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.545A pdb=" N GLU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.865A pdb=" N THR A 523 " --> pdb=" O HIS A 519 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 557 Processing helix chain 'A' and resid 585 through 592 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'B' and resid 131 through 137 removed outlier: 4.041A pdb=" N ARG B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 147 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.681A pdb=" N THR B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.726A pdb=" N ALA B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 323 through 334 Proline residue: B 330 - end of helix Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 374 through 379 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.781A pdb=" N THR B 419 " --> pdb=" O TYR B 415 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 420' Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.645A pdb=" N THR B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 removed outlier: 4.605A pdb=" N LYS B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 498 Processing helix chain 'B' and resid 502 through 517 Proline residue: B 508 - end of helix removed outlier: 5.244A pdb=" N VAL B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 512 " --> pdb=" O PRO B 508 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 517 " --> pdb=" O THR B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 527 removed outlier: 3.859A pdb=" N HIS B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 526 " --> pdb=" O TYR B 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.553A pdb=" N ILE C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Proline residue: C 18 - end of helix Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'D' and resid 53 through 63 Proline residue: D 57 - end of helix removed outlier: 5.032A pdb=" N THR D 60 " --> pdb=" O PRO D 57 " (cutoff:3.500A) Proline residue: D 61 - end of helix Processing helix chain 'D' and resid 68 through 83 Processing helix chain 'D' and resid 89 through 112 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 140 through 161 Processing helix chain 'D' and resid 181 through 211 removed outlier: 4.070A pdb=" N GLN D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Proline residue: D 192 - end of helix Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 306 through 318 removed outlier: 3.810A pdb=" N GLU D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 327 through 348 removed outlier: 3.948A pdb=" N HIS D 331 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 420 removed outlier: 3.690A pdb=" N ASN D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA D 408 " --> pdb=" O HIS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 441 removed outlier: 4.246A pdb=" N ILE D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR D 441 " --> pdb=" O VAL D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 448 No H-bonds generated for 'chain 'D' and resid 445 through 448' Processing helix chain 'E' and resid 16 through 22 Processing helix chain 'E' and resid 25 through 32 removed outlier: 3.621A pdb=" N ILE E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.900A pdb=" N GLU E 67 " --> pdb=" O VAL E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 90 through 95 Processing helix chain 'E' and resid 100 through 108 Processing helix chain 'E' and resid 153 through 165 Processing helix chain 'F' and resid 21 through 28 removed outlier: 3.698A pdb=" N ASN F 28 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 95 Processing helix chain 'F' and resid 100 through 102 No H-bonds generated for 'chain 'F' and resid 100 through 102' Processing helix chain 'F' and resid 110 through 117 Processing helix chain 'F' and resid 145 through 147 No H-bonds generated for 'chain 'F' and resid 145 through 147' Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 197 through 201 Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 265 through 274 removed outlier: 4.428A pdb=" N LEU F 271 " --> pdb=" O GLY F 267 " (cutoff:3.500A) Proline residue: F 272 - end of helix Processing helix chain 'F' and resid 296 through 311 removed outlier: 3.640A pdb=" N ALA F 310 " --> pdb=" O GLU F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 336 Processing helix chain 'F' and resid 350 through 366 Proline residue: F 362 - end of helix removed outlier: 4.972A pdb=" N GLN F 366 " --> pdb=" O PRO F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 379 removed outlier: 3.746A pdb=" N ILE F 377 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F 378 " --> pdb=" O HIS F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 393 No H-bonds generated for 'chain 'F' and resid 390 through 393' Processing helix chain 'F' and resid 395 through 407 Processing helix chain 'F' and resid 437 through 450 removed outlier: 3.545A pdb=" N GLU F 447 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE F 448 " --> pdb=" O ASN F 444 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 449 " --> pdb=" O LEU F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 502 Processing helix chain 'F' and resid 514 through 517 Processing helix chain 'F' and resid 519 through 532 removed outlier: 3.865A pdb=" N THR F 523 " --> pdb=" O HIS F 519 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER F 532 " --> pdb=" O LEU F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 557 Processing helix chain 'F' and resid 585 through 592 Processing helix chain 'F' and resid 606 through 609 No H-bonds generated for 'chain 'F' and resid 606 through 609' Processing helix chain 'F' and resid 652 through 659 Processing helix chain 'G' and resid 131 through 137 removed outlier: 4.041A pdb=" N ARG G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 147 Processing helix chain 'G' and resid 154 through 160 Processing helix chain 'G' and resid 174 through 182 Processing helix chain 'G' and resid 204 through 211 removed outlier: 3.681A pdb=" N THR G 208 " --> pdb=" O MET G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 227 Processing helix chain 'G' and resid 241 through 255 removed outlier: 3.726A pdb=" N ALA G 252 " --> pdb=" O LYS G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 283 through 285 No H-bonds generated for 'chain 'G' and resid 283 through 285' Processing helix chain 'G' and resid 287 through 294 Processing helix chain 'G' and resid 313 through 315 No H-bonds generated for 'chain 'G' and resid 313 through 315' Processing helix chain 'G' and resid 323 through 334 Proline residue: G 330 - end of helix Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 374 through 379 Processing helix chain 'G' and resid 415 through 420 removed outlier: 3.781A pdb=" N THR G 419 " --> pdb=" O TYR G 415 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA G 420 " --> pdb=" O GLU G 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 415 through 420' Processing helix chain 'G' and resid 439 through 452 removed outlier: 3.645A pdb=" N THR G 450 " --> pdb=" O PHE G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 476 removed outlier: 4.605A pdb=" N LYS G 466 " --> pdb=" O ARG G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 498 Processing helix chain 'G' and resid 502 through 517 Proline residue: G 508 - end of helix removed outlier: 5.244A pdb=" N VAL G 511 " --> pdb=" O ALA G 507 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE G 512 " --> pdb=" O PRO G 508 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR G 514 " --> pdb=" O PRO G 510 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR G 517 " --> pdb=" O THR G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 527 removed outlier: 3.859A pdb=" N HIS G 525 " --> pdb=" O GLU G 521 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE G 526 " --> pdb=" O TYR G 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 19 removed outlier: 3.553A pdb=" N ILE H 15 " --> pdb=" O LYS H 11 " (cutoff:3.500A) Proline residue: H 18 - end of helix Processing helix chain 'H' and resid 27 through 35 Processing helix chain 'H' and resid 42 through 52 Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'I' and resid 53 through 63 Proline residue: I 57 - end of helix removed outlier: 5.032A pdb=" N THR I 60 " --> pdb=" O PRO I 57 " (cutoff:3.500A) Proline residue: I 61 - end of helix Processing helix chain 'I' and resid 68 through 83 Processing helix chain 'I' and resid 89 through 112 Processing helix chain 'I' and resid 116 through 120 Processing helix chain 'I' and resid 132 through 138 Processing helix chain 'I' and resid 140 through 161 Processing helix chain 'I' and resid 181 through 211 removed outlier: 4.070A pdb=" N GLN I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU I 191 " --> pdb=" O ILE I 187 " (cutoff:3.500A) Proline residue: I 192 - end of helix Processing helix chain 'I' and resid 215 through 217 No H-bonds generated for 'chain 'I' and resid 215 through 217' Processing helix chain 'I' and resid 280 through 282 No H-bonds generated for 'chain 'I' and resid 280 through 282' Processing helix chain 'I' and resid 293 through 299 Processing helix chain 'I' and resid 306 through 318 removed outlier: 3.810A pdb=" N GLU I 311 " --> pdb=" O GLU I 307 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU I 314 " --> pdb=" O LYS I 310 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET I 318 " --> pdb=" O LEU I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 322 No H-bonds generated for 'chain 'I' and resid 320 through 322' Processing helix chain 'I' and resid 327 through 348 removed outlier: 3.948A pdb=" N HIS I 331 " --> pdb=" O LEU I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 401 through 420 removed outlier: 3.690A pdb=" N ASN I 405 " --> pdb=" O ALA I 401 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE I 407 " --> pdb=" O GLY I 403 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA I 408 " --> pdb=" O HIS I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 441 removed outlier: 4.246A pdb=" N ILE I 438 " --> pdb=" O LEU I 434 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR I 441 " --> pdb=" O VAL I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 448 No H-bonds generated for 'chain 'I' and resid 445 through 448' Processing helix chain 'J' and resid 16 through 22 Processing helix chain 'J' and resid 25 through 32 removed outlier: 3.621A pdb=" N ILE J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 74 removed outlier: 3.900A pdb=" N GLU J 67 " --> pdb=" O VAL J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 90 through 95 Processing helix chain 'J' and resid 100 through 108 Processing helix chain 'J' and resid 153 through 165 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= C, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= D, first strand: chain 'A' and resid 507 through 511 removed outlier: 6.004A pdb=" N LEU A 382 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE A 510 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 384 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS A 411 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR A 385 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET A 413 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN A 414 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP A 429 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 192 through 195 removed outlier: 9.087A pdb=" N CYS B 193 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR B 233 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA B 195 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR B 235 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS B 272 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE B 234 " --> pdb=" O HIS B 272 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS B 274 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS B 236 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS B 276 " --> pdb=" O CYS B 236 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 364 through 369 removed outlier: 3.509A pdb=" N VAL B 368 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA B 393 " --> pdb=" O MET B 433 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 5 through 8 removed outlier: 3.543A pdb=" N PHE D 5 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 33 " --> pdb=" O MET D 24 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 226 through 230 Processing sheet with id= I, first strand: chain 'D' and resid 264 through 267 Processing sheet with id= J, first strand: chain 'D' and resid 369 through 376 Processing sheet with id= K, first strand: chain 'E' and resid 7 through 10 removed outlier: 6.251A pdb=" N TYR E 78 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU E 56 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL E 80 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL E 144 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= M, first strand: chain 'F' and resid 141 through 143 Processing sheet with id= N, first strand: chain 'F' and resid 317 through 319 Processing sheet with id= O, first strand: chain 'F' and resid 507 through 511 removed outlier: 6.004A pdb=" N LEU F 382 " --> pdb=" O ILE F 508 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE F 510 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE F 384 " --> pdb=" O ILE F 510 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS F 411 " --> pdb=" O ILE F 383 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR F 385 " --> pdb=" O LYS F 411 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET F 413 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN F 414 " --> pdb=" O ASP F 427 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP F 429 " --> pdb=" O ASN F 414 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 192 through 195 removed outlier: 9.087A pdb=" N CYS G 193 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR G 233 " --> pdb=" O CYS G 193 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA G 195 " --> pdb=" O TYR G 233 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR G 235 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS G 272 " --> pdb=" O GLY G 232 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE G 234 " --> pdb=" O HIS G 272 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS G 274 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS G 236 " --> pdb=" O HIS G 274 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS G 276 " --> pdb=" O CYS G 236 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'G' and resid 364 through 369 removed outlier: 3.509A pdb=" N VAL G 368 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA G 393 " --> pdb=" O MET G 433 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 5 through 8 removed outlier: 3.543A pdb=" N PHE I 5 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU I 33 " --> pdb=" O MET I 24 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 226 through 230 Processing sheet with id= T, first strand: chain 'I' and resid 264 through 267 Processing sheet with id= U, first strand: chain 'I' and resid 369 through 376 Processing sheet with id= V, first strand: chain 'J' and resid 7 through 10 removed outlier: 6.251A pdb=" N TYR J 78 " --> pdb=" O GLY J 54 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU J 56 " --> pdb=" O TYR J 78 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL J 80 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL J 144 " --> pdb=" O ALA J 81 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2325 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: 8.60 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.38: 10516 1.38 - 1.62: 17772 1.62 - 1.86: 314 1.86 - 2.10: 0 2.10 - 2.34: 160 Bond restraints: 28762 Sorted by residual: bond pdb=" C2 FCO D 502 " pdb="FE FCO D 502 " ideal model delta sigma weight residual 1.939 1.792 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C2 FCO I 502 " pdb="FE FCO I 502 " ideal model delta sigma weight residual 1.939 1.792 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C1 FCO D 502 " pdb="FE FCO D 502 " ideal model delta sigma weight residual 1.940 1.796 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C1 FCO I 502 " pdb="FE FCO I 502 " ideal model delta sigma weight residual 1.940 1.796 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C3N NAD B 701 " pdb=" C4N NAD B 701 " ideal model delta sigma weight residual 1.390 1.485 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 28757 not shown) Histogram of bond angle deviations from ideal: 71.35 - 92.86: 162 92.86 - 114.36: 17771 114.36 - 135.87: 21075 135.87 - 157.38: 0 157.38 - 178.89: 6 Bond angle restraints: 39014 Sorted by residual: angle pdb=" C1 FCO I 502 " pdb="FE FCO I 502 " pdb=" C3 FCO I 502 " ideal model delta sigma weight residual 180.00 97.67 82.33 3.00e+00 1.11e-01 7.53e+02 angle pdb=" C1 FCO D 502 " pdb="FE FCO D 502 " pdb=" C3 FCO D 502 " ideal model delta sigma weight residual 180.00 97.67 82.33 3.00e+00 1.11e-01 7.53e+02 angle pdb=" S1 FES B 704 " pdb="FE2 FES B 704 " pdb=" S2 FES B 704 " ideal model delta sigma weight residual 104.33 83.40 20.93 1.14e+00 7.69e-01 3.37e+02 angle pdb=" S1 FES G 704 " pdb="FE2 FES G 704 " pdb=" S2 FES G 704 " ideal model delta sigma weight residual 104.33 83.40 20.93 1.14e+00 7.69e-01 3.37e+02 angle pdb=" S1 FES B 704 " pdb="FE1 FES B 704 " pdb=" S2 FES B 704 " ideal model delta sigma weight residual 104.33 83.16 21.17 1.20e+00 6.94e-01 3.11e+02 ... (remaining 39009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 16659 35.22 - 70.43: 682 70.43 - 105.65: 53 105.65 - 140.87: 0 140.87 - 176.08: 2 Dihedral angle restraints: 17396 sinusoidal: 7158 harmonic: 10238 Sorted by residual: dihedral pdb=" C10 FMN G 703 " pdb=" C1' FMN G 703 " pdb=" N10 FMN G 703 " pdb=" C2' FMN G 703 " ideal model delta sinusoidal sigma weight residual 257.59 81.51 176.08 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C10 FMN B 703 " pdb=" C1' FMN B 703 " pdb=" N10 FMN B 703 " pdb=" C2' FMN B 703 " ideal model delta sinusoidal sigma weight residual 257.59 81.51 176.08 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA THR I 86 " pdb=" C THR I 86 " pdb=" N ILE I 87 " pdb=" CA ILE I 87 " ideal model delta harmonic sigma weight residual -180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 17393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3344 0.062 - 0.123: 865 0.123 - 0.185: 133 0.185 - 0.246: 6 0.246 - 0.308: 10 Chirality restraints: 4358 Sorted by residual: chirality pdb=" CB VAL F 149 " pdb=" CA VAL F 149 " pdb=" CG1 VAL F 149 " pdb=" CG2 VAL F 149 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB VAL A 149 " pdb=" CA VAL A 149 " pdb=" CG1 VAL A 149 " pdb=" CG2 VAL A 149 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb="FE2 SF4 G 702 " pdb=" S1 SF4 G 702 " pdb=" S3 SF4 G 702 " pdb=" S4 SF4 G 702 " both_signs ideal model delta sigma weight residual False 10.55 10.85 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 4355 not shown) Planarity restraints: 4988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD G 701 " 0.108 2.00e-02 2.50e+03 9.14e-02 1.67e+02 pdb=" C2N NAD G 701 " -0.009 2.00e-02 2.50e+03 pdb=" C3N NAD G 701 " 0.010 2.00e-02 2.50e+03 pdb=" C4N NAD G 701 " 0.128 2.00e-02 2.50e+03 pdb=" C5N NAD G 701 " 0.039 2.00e-02 2.50e+03 pdb=" C6N NAD G 701 " -0.179 2.00e-02 2.50e+03 pdb=" C7N NAD G 701 " -0.062 2.00e-02 2.50e+03 pdb=" N1N NAD G 701 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 701 " 0.108 2.00e-02 2.50e+03 9.14e-02 1.67e+02 pdb=" C2N NAD B 701 " -0.009 2.00e-02 2.50e+03 pdb=" C3N NAD B 701 " 0.010 2.00e-02 2.50e+03 pdb=" C4N NAD B 701 " 0.128 2.00e-02 2.50e+03 pdb=" C5N NAD B 701 " 0.039 2.00e-02 2.50e+03 pdb=" C6N NAD B 701 " -0.179 2.00e-02 2.50e+03 pdb=" C7N NAD B 701 " -0.062 2.00e-02 2.50e+03 pdb=" N1N NAD B 701 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 125 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO F 126 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 126 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 126 " 0.033 5.00e-02 4.00e+02 ... (remaining 4985 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 674 2.68 - 3.23: 27098 3.23 - 3.79: 44897 3.79 - 4.34: 63384 4.34 - 4.90: 101911 Nonbonded interactions: 237964 Sorted by model distance: nonbonded pdb=" OH TYR F 574 " pdb=" OE1 GLN F 600 " model vdw 2.121 2.440 nonbonded pdb=" OH TYR A 574 " pdb=" OE1 GLN A 600 " model vdw 2.121 2.440 nonbonded pdb=" NH2 ARG A 286 " pdb=" O ILE I 251 " model vdw 2.157 2.520 nonbonded pdb=" O ILE D 251 " pdb=" NH2 ARG F 286 " model vdw 2.157 2.520 nonbonded pdb=" O MET B 494 " pdb=" OG1 THR B 498 " model vdw 2.169 2.440 ... (remaining 237959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.020 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 75.530 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.220 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:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.006 0.147 28762 Z= 0.388 Angle : 1.076 82.328 39014 Z= 0.626 Chirality : 0.055 0.308 4358 Planarity : 0.006 0.091 4988 Dihedral : 17.539 176.082 10836 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 6.14 % Allowed : 22.16 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -3.78 (0.12), residues: 3554 helix: -1.99 (0.12), residues: 1382 sheet: -2.08 (0.24), residues: 386 loop : -3.08 (0.12), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 326 HIS 0.005 0.001 HIS A 165 PHE 0.019 0.001 PHE I 47 TYR 0.016 0.001 TYR B 125 ARG 0.004 0.000 ARG F 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 971 time to evaluate : 3.094 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: A 14 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7832 (mmmt) REVERT: A 19 ASP cc_start: 0.7430 (p0) cc_final: 0.7221 (p0) REVERT: A 42 THR cc_start: 0.8257 (m) cc_final: 0.7909 (t) REVERT: A 60 MET cc_start: 0.7860 (mtm) cc_final: 0.7604 (mtm) REVERT: A 120 MET cc_start: 0.7895 (ttp) cc_final: 0.7676 (ttt) REVERT: A 133 GLU cc_start: 0.7075 (pt0) cc_final: 0.6829 (pt0) REVERT: A 309 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7923 (ttmt) REVERT: A 313 GLN cc_start: 0.7661 (mt0) cc_final: 0.7399 (pt0) REVERT: A 345 ILE cc_start: 0.8334 (mm) cc_final: 0.8033 (mm) REVERT: A 384 ILE cc_start: 0.8408 (mp) cc_final: 0.8040 (mm) REVERT: A 385 THR cc_start: 0.8220 (m) cc_final: 0.7761 (p) REVERT: A 413 MET cc_start: 0.6749 (ptp) cc_final: 0.5931 (ptp) REVERT: A 496 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6577 (pm20) REVERT: A 517 LYS cc_start: 0.7525 (pptt) cc_final: 0.7257 (pptt) REVERT: A 520 GLU cc_start: 0.6732 (mp0) cc_final: 0.6365 (mp0) REVERT: A 611 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8162 (pp) REVERT: B 153 GLU cc_start: 0.7378 (tp30) cc_final: 0.7153 (tp30) REVERT: B 167 ARG cc_start: 0.8551 (mmt-90) cc_final: 0.8341 (mpt180) REVERT: B 210 GLU cc_start: 0.6091 (mt-10) cc_final: 0.5695 (mt-10) REVERT: B 212 ASP cc_start: 0.7523 (p0) cc_final: 0.7323 (p0) REVERT: B 222 ILE cc_start: 0.8877 (mm) cc_final: 0.8661 (mt) REVERT: B 231 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6388 (mm-30) REVERT: B 271 PHE cc_start: 0.7875 (t80) cc_final: 0.7625 (t80) REVERT: B 313 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7733 (mp) REVERT: B 345 THR cc_start: 0.6022 (OUTLIER) cc_final: 0.5790 (p) REVERT: B 356 LEU cc_start: 0.7886 (tp) cc_final: 0.7667 (tt) REVERT: B 453 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6935 (mm-30) REVERT: B 529 LYS cc_start: 0.8240 (mptm) cc_final: 0.8000 (tppp) REVERT: D 23 VAL cc_start: 0.8377 (t) cc_final: 0.8060 (m) REVERT: D 51 ARG cc_start: 0.7925 (mmm160) cc_final: 0.7686 (mmm160) REVERT: D 56 MET cc_start: 0.8098 (mmm) cc_final: 0.7842 (mmp) REVERT: D 111 PHE cc_start: 0.8365 (t80) cc_final: 0.8089 (t80) REVERT: D 115 SER cc_start: 0.8234 (p) cc_final: 0.8026 (t) REVERT: D 207 ASP cc_start: 0.6966 (m-30) cc_final: 0.6748 (m-30) REVERT: D 269 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7072 (mm-30) REVERT: D 290 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8250 (mtt180) REVERT: D 311 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6269 (mm-30) REVERT: D 346 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6635 (mt-10) REVERT: D 390 SER cc_start: 0.8015 (m) cc_final: 0.7620 (t) REVERT: E 30 ASP cc_start: 0.6832 (p0) cc_final: 0.6571 (p0) REVERT: E 174 GLU cc_start: 0.7143 (pm20) cc_final: 0.6845 (pm20) REVERT: F 42 THR cc_start: 0.8229 (m) cc_final: 0.7500 (t) REVERT: F 60 MET cc_start: 0.8002 (mtm) cc_final: 0.7783 (mtm) REVERT: F 90 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7296 (mm-30) REVERT: F 105 GLN cc_start: 0.7998 (mm110) cc_final: 0.7633 (mm-40) REVERT: F 120 MET cc_start: 0.7726 (ttp) cc_final: 0.7392 (ttt) REVERT: F 133 GLU cc_start: 0.7033 (pt0) cc_final: 0.6687 (pt0) REVERT: F 142 MET cc_start: 0.7813 (ttt) cc_final: 0.7590 (ttm) REVERT: F 156 ARG cc_start: 0.7380 (mmt90) cc_final: 0.7016 (mmt90) REVERT: F 170 GLU cc_start: 0.7169 (tt0) cc_final: 0.6952 (tt0) REVERT: F 177 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7625 (ttpp) REVERT: F 256 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6474 (mm-30) REVERT: F 306 GLU cc_start: 0.6683 (tp30) cc_final: 0.6329 (tp30) REVERT: F 309 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7682 (ttmt) REVERT: F 319 ILE cc_start: 0.8224 (mt) cc_final: 0.8023 (mt) REVERT: F 345 ILE cc_start: 0.8362 (mm) cc_final: 0.8014 (mm) REVERT: F 381 ASP cc_start: 0.7492 (m-30) cc_final: 0.7287 (m-30) REVERT: F 384 ILE cc_start: 0.8313 (mp) cc_final: 0.7919 (mm) REVERT: F 385 THR cc_start: 0.8156 (m) cc_final: 0.7688 (p) REVERT: F 413 MET cc_start: 0.6799 (ptp) cc_final: 0.5929 (ptp) REVERT: F 429 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6723 (p0) REVERT: F 440 LYS cc_start: 0.7609 (tptt) cc_final: 0.7254 (mptt) REVERT: F 496 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: F 521 LEU cc_start: 0.8079 (tp) cc_final: 0.7858 (tp) REVERT: F 562 ASN cc_start: 0.8055 (m110) cc_final: 0.7836 (m-40) REVERT: F 611 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8263 (pt) REVERT: F 623 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7049 (mt-10) REVERT: F 638 LEU cc_start: 0.8574 (mt) cc_final: 0.8300 (mp) REVERT: G 179 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7224 (tm-30) REVERT: G 183 LYS cc_start: 0.8238 (mttm) cc_final: 0.7999 (mttm) REVERT: G 191 VAL cc_start: 0.8568 (m) cc_final: 0.8297 (t) REVERT: G 212 ASP cc_start: 0.7722 (p0) cc_final: 0.6883 (p0) REVERT: G 217 ILE cc_start: 0.7652 (mm) cc_final: 0.7445 (mp) REVERT: G 271 PHE cc_start: 0.7961 (t80) cc_final: 0.7506 (t80) REVERT: G 313 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7764 (mp) REVERT: G 452 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7245 (mtm-85) REVERT: G 527 LYS cc_start: 0.8140 (mmtp) cc_final: 0.7864 (mmtp) REVERT: I 7 LEU cc_start: 0.8459 (mt) cc_final: 0.7949 (mp) REVERT: I 51 ARG cc_start: 0.7917 (mmm160) cc_final: 0.7673 (mmm160) REVERT: I 56 MET cc_start: 0.8138 (mmm) cc_final: 0.7887 (mmp) REVERT: I 111 PHE cc_start: 0.8307 (t80) cc_final: 0.8039 (t80) REVERT: I 115 SER cc_start: 0.8210 (p) cc_final: 0.7994 (t) REVERT: I 151 LYS cc_start: 0.7851 (tttm) cc_final: 0.6896 (tttm) REVERT: I 155 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: I 194 MET cc_start: 0.7920 (mmt) cc_final: 0.7689 (mmm) REVERT: I 207 ASP cc_start: 0.7099 (m-30) cc_final: 0.6831 (m-30) REVERT: I 310 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7786 (mtmm) REVERT: I 311 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6335 (mm-30) REVERT: I 390 SER cc_start: 0.8023 (m) cc_final: 0.7629 (t) REVERT: J 128 GLU cc_start: 0.6921 (tp30) cc_final: 0.6676 (tp30) REVERT: J 137 ASP cc_start: 0.6743 (t0) cc_final: 0.6530 (t0) REVERT: J 174 GLU cc_start: 0.7152 (pm20) cc_final: 0.6881 (pm20) outliers start: 184 outliers final: 73 residues processed: 1079 average time/residue: 1.4088 time to fit residues: 1755.8168 Evaluate side-chains 977 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 894 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 PHE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 661 LYS Chi-restraints excluded: chain G residue 125 TYR Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 328 ASN Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 458 CYS Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 160 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 167 optimal weight: 0.0570 chunk 205 optimal weight: 3.9990 chunk 319 optimal weight: 0.6980 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 105 GLN A 118 HIS A 145 HIS A 146 ASN A 175 GLN A 262 GLN A 313 GLN A 391 GLN A 414 ASN A 556 ASN ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS B 253 GLN B 274 HIS B 328 ASN B 362 ASN D 166 HIS D 210 GLN D 298 ASN D 386 GLN D 425 ASN F 97 ASN F 105 GLN F 118 HIS F 145 HIS F 146 ASN F 175 GLN F 391 GLN F 414 ASN ** F 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS G 253 GLN G 274 HIS G 328 ASN G 362 ASN I 166 HIS I 210 GLN I 425 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28762 Z= 0.209 Angle : 0.618 12.249 39014 Z= 0.309 Chirality : 0.045 0.207 4358 Planarity : 0.005 0.055 4988 Dihedral : 9.970 175.069 4170 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.01 % Favored : 92.94 % Rotamer: Outliers : 6.64 % Allowed : 25.20 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -2.54 (0.13), residues: 3554 helix: -0.86 (0.13), residues: 1400 sheet: -1.57 (0.26), residues: 366 loop : -2.42 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 168 HIS 0.009 0.001 HIS B 116 PHE 0.021 0.001 PHE G 518 TYR 0.013 0.001 TYR I 420 ARG 0.006 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 912 time to evaluate : 3.129 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: A 60 MET cc_start: 0.7863 (mtm) cc_final: 0.7643 (mtm) REVERT: A 120 MET cc_start: 0.7914 (ttp) cc_final: 0.7639 (ttt) REVERT: A 133 GLU cc_start: 0.7039 (pt0) cc_final: 0.6805 (pt0) REVERT: A 306 GLU cc_start: 0.6754 (tp30) cc_final: 0.6294 (tp30) REVERT: A 309 LYS cc_start: 0.8223 (ttmt) cc_final: 0.8001 (ttmt) REVERT: A 322 SER cc_start: 0.7841 (p) cc_final: 0.7636 (t) REVERT: A 345 ILE cc_start: 0.8441 (mm) cc_final: 0.8062 (mm) REVERT: A 381 ASP cc_start: 0.7367 (m-30) cc_final: 0.7023 (m-30) REVERT: A 385 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7817 (p) REVERT: A 399 SER cc_start: 0.8118 (m) cc_final: 0.7883 (t) REVERT: A 413 MET cc_start: 0.6800 (ptp) cc_final: 0.6189 (ptp) REVERT: A 517 LYS cc_start: 0.7527 (pptt) cc_final: 0.7235 (pptt) REVERT: A 520 GLU cc_start: 0.6716 (mp0) cc_final: 0.6325 (mp0) REVERT: A 594 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7512 (m) REVERT: A 611 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8203 (pp) REVERT: B 204 MET cc_start: 0.6075 (mpp) cc_final: 0.5848 (mpp) REVERT: B 212 ASP cc_start: 0.7443 (p0) cc_final: 0.6897 (p0) REVERT: B 231 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6411 (mm-30) REVERT: B 316 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8195 (mmtm) REVERT: B 319 ASN cc_start: 0.8068 (t0) cc_final: 0.7768 (t0) REVERT: B 356 LEU cc_start: 0.7708 (tp) cc_final: 0.7477 (tt) REVERT: B 427 SER cc_start: 0.8137 (m) cc_final: 0.7549 (t) REVERT: B 453 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6919 (mm-30) REVERT: B 526 ILE cc_start: 0.8196 (mm) cc_final: 0.7904 (mm) REVERT: C 11 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7700 (tmtp) REVERT: D 10 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7612 (p0) REVERT: D 16 GLU cc_start: 0.5933 (tm-30) cc_final: 0.5559 (tm-30) REVERT: D 111 PHE cc_start: 0.8369 (t80) cc_final: 0.7921 (t80) REVERT: D 115 SER cc_start: 0.8277 (p) cc_final: 0.8013 (t) REVERT: D 207 ASP cc_start: 0.6998 (m-30) cc_final: 0.6733 (m-30) REVERT: D 214 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6531 (tm-30) REVERT: D 269 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7055 (mm-30) REVERT: D 311 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6298 (mm-30) REVERT: D 390 SER cc_start: 0.8101 (m) cc_final: 0.7732 (t) REVERT: E 30 ASP cc_start: 0.6801 (p0) cc_final: 0.6462 (p0) REVERT: E 174 GLU cc_start: 0.7122 (pm20) cc_final: 0.6907 (pm20) REVERT: F 42 THR cc_start: 0.8346 (m) cc_final: 0.8029 (t) REVERT: F 60 MET cc_start: 0.8021 (mtm) cc_final: 0.7796 (mtm) REVERT: F 120 MET cc_start: 0.7758 (ttp) cc_final: 0.7459 (ttt) REVERT: F 133 GLU cc_start: 0.6986 (pt0) cc_final: 0.6689 (pt0) REVERT: F 138 ASP cc_start: 0.7714 (t0) cc_final: 0.7454 (t0) REVERT: F 218 ARG cc_start: 0.7278 (mtt90) cc_final: 0.7067 (mtt90) REVERT: F 306 GLU cc_start: 0.6672 (tp30) cc_final: 0.6153 (tp30) REVERT: F 309 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7725 (ttmt) REVERT: F 322 SER cc_start: 0.7929 (p) cc_final: 0.7707 (t) REVERT: F 384 ILE cc_start: 0.8249 (mp) cc_final: 0.7950 (mm) REVERT: F 385 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7737 (p) REVERT: F 413 MET cc_start: 0.6882 (ptp) cc_final: 0.6055 (ptp) REVERT: F 562 ASN cc_start: 0.8054 (m110) cc_final: 0.7809 (m-40) REVERT: F 594 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7356 (m) REVERT: F 611 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8410 (pp) REVERT: F 638 LEU cc_start: 0.8592 (mt) cc_final: 0.8269 (mp) REVERT: G 179 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7214 (tm-30) REVERT: G 183 LYS cc_start: 0.8189 (mttm) cc_final: 0.7905 (mttm) REVERT: G 217 ILE cc_start: 0.7679 (mm) cc_final: 0.7456 (mp) REVERT: G 271 PHE cc_start: 0.7927 (t80) cc_final: 0.7575 (t80) REVERT: G 300 MET cc_start: 0.7467 (mtp) cc_final: 0.7243 (mtp) REVERT: G 313 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7608 (mp) REVERT: G 319 ASN cc_start: 0.8143 (t0) cc_final: 0.7902 (t0) REVERT: G 494 MET cc_start: 0.7672 (tmm) cc_final: 0.7204 (tmm) REVERT: G 521 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7268 (OUTLIER) REVERT: G 526 ILE cc_start: 0.8169 (mm) cc_final: 0.7828 (mm) REVERT: G 527 LYS cc_start: 0.8077 (mmtp) cc_final: 0.7816 (mmtp) REVERT: G 531 CYS cc_start: 0.7405 (t) cc_final: 0.6936 (t) REVERT: H 11 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7837 (tmtp) REVERT: I 6 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7410 (mtmm) REVERT: I 7 LEU cc_start: 0.8470 (mt) cc_final: 0.8082 (mt) REVERT: I 10 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7640 (p0) REVERT: I 16 GLU cc_start: 0.6051 (tm-30) cc_final: 0.5734 (tm-30) REVERT: I 56 MET cc_start: 0.8113 (mmm) cc_final: 0.7871 (mmp) REVERT: I 111 PHE cc_start: 0.8301 (t80) cc_final: 0.8014 (t80) REVERT: I 115 SER cc_start: 0.8225 (p) cc_final: 0.7982 (t) REVERT: I 151 LYS cc_start: 0.7925 (tttm) cc_final: 0.6704 (tttp) REVERT: I 155 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: I 214 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6558 (tm-30) REVERT: I 311 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6393 (mm-30) REVERT: I 390 SER cc_start: 0.8043 (m) cc_final: 0.7742 (t) REVERT: J 87 VAL cc_start: 0.8483 (t) cc_final: 0.8278 (t) REVERT: J 128 GLU cc_start: 0.6948 (tp30) cc_final: 0.6691 (tp30) REVERT: J 137 ASP cc_start: 0.6800 (t0) cc_final: 0.6597 (t0) REVERT: J 174 GLU cc_start: 0.7145 (pm20) cc_final: 0.6942 (pm20) outliers start: 199 outliers final: 86 residues processed: 1024 average time/residue: 1.4063 time to fit residues: 1666.6685 Evaluate side-chains 974 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 877 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 661 LYS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 354 ILE Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 160 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 0.0770 chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 320 optimal weight: 0.5980 chunk 345 optimal weight: 4.9990 chunk 285 optimal weight: 0.5980 chunk 317 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 262 GLN A 556 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS D 298 ASN E 18 HIS F 105 GLN F 152 GLN F 175 GLN ** F 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS I 263 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28762 Z= 0.211 Angle : 0.602 12.832 39014 Z= 0.299 Chirality : 0.045 0.233 4358 Planarity : 0.005 0.054 4988 Dihedral : 9.314 175.145 4115 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.08 % Rotamer: Outliers : 7.01 % Allowed : 25.60 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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 (0.13), residues: 3554 helix: -0.39 (0.14), residues: 1396 sheet: -1.32 (0.27), residues: 378 loop : -2.19 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 271 HIS 0.005 0.001 HIS F 165 PHE 0.022 0.001 PHE B 518 TYR 0.010 0.001 TYR G 125 ARG 0.008 0.000 ARG G 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 888 time to evaluate : 3.274 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: A 60 MET cc_start: 0.7879 (mtm) cc_final: 0.7614 (mtm) REVERT: A 86 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7408 (ttp-170) REVERT: A 120 MET cc_start: 0.7918 (ttp) cc_final: 0.7545 (ttt) REVERT: A 133 GLU cc_start: 0.7039 (pt0) cc_final: 0.6820 (pt0) REVERT: A 306 GLU cc_start: 0.6805 (tp30) cc_final: 0.6257 (tp30) REVERT: A 309 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7988 (ttmt) REVERT: A 322 SER cc_start: 0.7946 (p) cc_final: 0.7700 (t) REVERT: A 361 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6466 (mpp) REVERT: A 381 ASP cc_start: 0.7332 (m-30) cc_final: 0.6997 (m-30) REVERT: A 385 THR cc_start: 0.8235 (m) cc_final: 0.7697 (p) REVERT: A 429 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6726 (p0) REVERT: A 501 LEU cc_start: 0.7146 (tm) cc_final: 0.6912 (tt) REVERT: A 517 LYS cc_start: 0.7554 (pptt) cc_final: 0.7200 (pptt) REVERT: A 520 GLU cc_start: 0.6765 (mp0) cc_final: 0.6354 (mp0) REVERT: A 594 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7534 (m) REVERT: A 611 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8241 (pp) REVERT: B 212 ASP cc_start: 0.7355 (p0) cc_final: 0.6495 (p0) REVERT: B 218 GLU cc_start: 0.6670 (tt0) cc_final: 0.6338 (tt0) REVERT: B 222 ILE cc_start: 0.8772 (mt) cc_final: 0.8509 (mp) REVERT: B 231 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6439 (mm-30) REVERT: B 249 ILE cc_start: 0.8550 (pp) cc_final: 0.8266 (pt) REVERT: B 316 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8181 (mmtm) REVERT: B 349 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7968 (mmtt) REVERT: B 356 LEU cc_start: 0.7701 (tp) cc_final: 0.7461 (tt) REVERT: B 404 LEU cc_start: 0.8141 (mm) cc_final: 0.7905 (mt) REVERT: B 407 GLU cc_start: 0.6903 (pm20) cc_final: 0.6682 (pm20) REVERT: B 453 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6900 (mm-30) REVERT: B 494 MET cc_start: 0.7676 (tmm) cc_final: 0.7420 (tmt) REVERT: C 10 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6506 (pm20) REVERT: C 11 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7707 (tmtp) REVERT: D 10 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7763 (p0) REVERT: D 16 GLU cc_start: 0.5987 (tm-30) cc_final: 0.5554 (tm-30) REVERT: D 111 PHE cc_start: 0.8394 (t80) cc_final: 0.8095 (t80) REVERT: D 115 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.8002 (t) REVERT: D 207 ASP cc_start: 0.7012 (m-30) cc_final: 0.6750 (m-30) REVERT: D 214 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6516 (tm-30) REVERT: D 311 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6308 (mm-30) REVERT: D 337 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6293 (mm-30) REVERT: D 390 SER cc_start: 0.8070 (m) cc_final: 0.7735 (t) REVERT: F 5 THR cc_start: 0.8440 (p) cc_final: 0.8207 (t) REVERT: F 42 THR cc_start: 0.8388 (m) cc_final: 0.7446 (t) REVERT: F 60 MET cc_start: 0.8042 (mtm) cc_final: 0.7817 (mtm) REVERT: F 120 MET cc_start: 0.7764 (ttp) cc_final: 0.7485 (ttt) REVERT: F 133 GLU cc_start: 0.6973 (pt0) cc_final: 0.6564 (pt0) REVERT: F 138 ASP cc_start: 0.7689 (t0) cc_final: 0.7427 (t0) REVERT: F 156 ARG cc_start: 0.7268 (mmt90) cc_final: 0.6847 (mmt90) REVERT: F 177 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7660 (ttpp) REVERT: F 306 GLU cc_start: 0.6729 (tp30) cc_final: 0.6149 (tp30) REVERT: F 309 LYS cc_start: 0.7990 (ttmt) cc_final: 0.7721 (ttmt) REVERT: F 322 SER cc_start: 0.7991 (p) cc_final: 0.7720 (t) REVERT: F 384 ILE cc_start: 0.8175 (mp) cc_final: 0.7896 (mm) REVERT: F 385 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7758 (p) REVERT: F 413 MET cc_start: 0.6846 (ptp) cc_final: 0.6037 (ptp) REVERT: F 429 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6767 (p0) REVERT: F 562 ASN cc_start: 0.8041 (m110) cc_final: 0.7810 (m-40) REVERT: F 568 GLU cc_start: 0.7147 (mp0) cc_final: 0.6883 (mp0) REVERT: F 594 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7378 (m) REVERT: F 611 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8435 (pp) REVERT: F 638 LEU cc_start: 0.8572 (mt) cc_final: 0.8264 (mp) REVERT: G 179 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7250 (tm-30) REVERT: G 183 LYS cc_start: 0.8165 (mttm) cc_final: 0.7900 (mttm) REVERT: G 205 ASP cc_start: 0.6695 (t0) cc_final: 0.6396 (t0) REVERT: G 212 ASP cc_start: 0.7575 (p0) cc_final: 0.6780 (p0) REVERT: G 217 ILE cc_start: 0.7728 (mm) cc_final: 0.7438 (mp) REVERT: G 313 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7611 (mp) REVERT: G 316 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8210 (mmtm) REVERT: G 319 ASN cc_start: 0.8102 (t0) cc_final: 0.7861 (t0) REVERT: G 356 LEU cc_start: 0.7962 (tp) cc_final: 0.7676 (tt) REVERT: G 494 MET cc_start: 0.7681 (tmm) cc_final: 0.7312 (tmm) REVERT: G 531 CYS cc_start: 0.7229 (t) cc_final: 0.6781 (t) REVERT: H 10 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6730 (pm20) REVERT: H 11 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7786 (tmtp) REVERT: I 6 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7455 (mtmm) REVERT: I 7 LEU cc_start: 0.8449 (mt) cc_final: 0.8146 (mt) REVERT: I 10 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7746 (p0) REVERT: I 16 GLU cc_start: 0.6082 (tm-30) cc_final: 0.5684 (tm-30) REVERT: I 35 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7894 (mtp85) REVERT: I 56 MET cc_start: 0.8117 (mmm) cc_final: 0.7877 (mmp) REVERT: I 81 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6936 (mt-10) REVERT: I 111 PHE cc_start: 0.8345 (t80) cc_final: 0.8063 (t80) REVERT: I 115 SER cc_start: 0.8213 (p) cc_final: 0.7972 (t) REVERT: I 151 LYS cc_start: 0.7951 (tttm) cc_final: 0.6784 (ttmm) REVERT: I 155 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: I 214 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6522 (tm-30) REVERT: I 290 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8008 (mtt180) REVERT: I 307 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6229 (tm-30) REVERT: I 311 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6360 (mm-30) REVERT: I 390 SER cc_start: 0.8018 (m) cc_final: 0.7717 (t) REVERT: J 87 VAL cc_start: 0.8483 (t) cc_final: 0.8277 (t) REVERT: J 125 ASP cc_start: 0.6443 (t0) cc_final: 0.6069 (t0) REVERT: J 128 GLU cc_start: 0.6969 (tp30) cc_final: 0.6702 (tp30) outliers start: 210 outliers final: 109 residues processed: 1000 average time/residue: 1.4446 time to fit residues: 1667.2429 Evaluate side-chains 1000 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 870 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 625 SER Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 680 SER Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 354 ILE Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 160 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.9980 chunk 240 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 321 optimal weight: 0.0980 chunk 340 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 556 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN F 105 GLN F 175 GLN F 262 GLN ** F 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28762 Z= 0.291 Angle : 0.620 13.034 39014 Z= 0.309 Chirality : 0.047 0.177 4358 Planarity : 0.005 0.057 4988 Dihedral : 9.127 174.741 4103 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 6.84 % Allowed : 26.50 % Favored : 66.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.14), residues: 3554 helix: -0.27 (0.14), residues: 1412 sheet: -1.11 (0.28), residues: 376 loop : -2.09 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.006 0.001 HIS G 525 PHE 0.029 0.002 PHE B 446 TYR 0.013 0.001 TYR D 315 ARG 0.008 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 888 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8261 (p) cc_final: 0.7995 (t) REVERT: A 60 MET cc_start: 0.7923 (mtm) cc_final: 0.7694 (mtm) REVERT: A 69 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7781 (mm-40) REVERT: A 86 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7427 (ttp-170) REVERT: A 120 MET cc_start: 0.7919 (ttp) cc_final: 0.7585 (ttt) REVERT: A 309 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7979 (ttmt) REVERT: A 322 SER cc_start: 0.7984 (p) cc_final: 0.7713 (t) REVERT: A 345 ILE cc_start: 0.8368 (mm) cc_final: 0.7947 (mm) REVERT: A 381 ASP cc_start: 0.7345 (m-30) cc_final: 0.7010 (m-30) REVERT: A 408 ARG cc_start: 0.7290 (mtt90) cc_final: 0.6971 (mtt90) REVERT: A 413 MET cc_start: 0.6680 (ptp) cc_final: 0.6448 (ptt) REVERT: A 429 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6656 (p0) REVERT: A 517 LYS cc_start: 0.7570 (pptt) cc_final: 0.7210 (pptt) REVERT: A 520 GLU cc_start: 0.6799 (mp0) cc_final: 0.6331 (mp0) REVERT: A 611 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8252 (pp) REVERT: B 205 ASP cc_start: 0.6788 (t0) cc_final: 0.6305 (t0) REVERT: B 212 ASP cc_start: 0.7385 (p0) cc_final: 0.6524 (p0) REVERT: B 218 GLU cc_start: 0.6776 (tt0) cc_final: 0.6414 (tt0) REVERT: B 222 ILE cc_start: 0.8753 (mt) cc_final: 0.8537 (mp) REVERT: B 231 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6478 (mm-30) REVERT: B 271 PHE cc_start: 0.7871 (t80) cc_final: 0.7662 (t80) REVERT: B 316 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8210 (mmtm) REVERT: B 356 LEU cc_start: 0.7765 (tp) cc_final: 0.7522 (tt) REVERT: B 361 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.6044 (m) REVERT: B 387 ASN cc_start: 0.7555 (m-40) cc_final: 0.7287 (m-40) REVERT: B 453 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6852 (mm-30) REVERT: B 494 MET cc_start: 0.7708 (tmm) cc_final: 0.7461 (tmt) REVERT: C 10 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: C 11 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7727 (tmtp) REVERT: D 16 GLU cc_start: 0.6023 (tm-30) cc_final: 0.5573 (tm-30) REVERT: D 115 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7974 (t) REVERT: D 204 LEU cc_start: 0.8185 (tp) cc_final: 0.7962 (tt) REVERT: D 207 ASP cc_start: 0.7025 (m-30) cc_final: 0.6760 (m-30) REVERT: D 269 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6703 (mm-30) REVERT: D 311 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6329 (mm-30) REVERT: D 390 SER cc_start: 0.8056 (m) cc_final: 0.7712 (t) REVERT: E 65 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: F 5 THR cc_start: 0.8348 (p) cc_final: 0.8101 (t) REVERT: F 60 MET cc_start: 0.8082 (mtm) cc_final: 0.7850 (mtm) REVERT: F 120 MET cc_start: 0.7769 (ttp) cc_final: 0.7484 (ttt) REVERT: F 133 GLU cc_start: 0.6972 (pt0) cc_final: 0.6561 (pt0) REVERT: F 138 ASP cc_start: 0.7672 (t0) cc_final: 0.7421 (t0) REVERT: F 156 ARG cc_start: 0.7285 (mmt90) cc_final: 0.6925 (mmt90) REVERT: F 177 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7672 (ttpp) REVERT: F 306 GLU cc_start: 0.6781 (tp30) cc_final: 0.6141 (tp30) REVERT: F 309 LYS cc_start: 0.8025 (ttmt) cc_final: 0.7741 (ttmt) REVERT: F 322 SER cc_start: 0.8030 (p) cc_final: 0.7726 (t) REVERT: F 345 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7929 (mm) REVERT: F 385 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7741 (p) REVERT: F 411 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7591 (mtpp) REVERT: F 413 MET cc_start: 0.6844 (ptp) cc_final: 0.6234 (ptp) REVERT: F 429 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6760 (p0) REVERT: F 517 LYS cc_start: 0.7370 (pptt) cc_final: 0.7040 (pptt) REVERT: F 594 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7546 (m) REVERT: F 611 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8422 (pp) REVERT: F 638 LEU cc_start: 0.8581 (mt) cc_final: 0.8257 (mp) REVERT: F 688 ARG cc_start: 0.6596 (mtm110) cc_final: 0.6357 (mtm180) REVERT: G 179 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7279 (tm-30) REVERT: G 183 LYS cc_start: 0.8189 (mttm) cc_final: 0.7922 (mttm) REVERT: G 222 ILE cc_start: 0.8748 (mt) cc_final: 0.8478 (mp) REVERT: G 300 MET cc_start: 0.7547 (mtp) cc_final: 0.7303 (mtp) REVERT: G 313 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7687 (mp) REVERT: G 316 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8237 (mmtm) REVERT: G 319 ASN cc_start: 0.8140 (t0) cc_final: 0.7888 (t0) REVERT: G 333 ILE cc_start: 0.8479 (mm) cc_final: 0.8226 (tp) REVERT: G 531 CYS cc_start: 0.7183 (t) cc_final: 0.6761 (t) REVERT: H 10 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: H 11 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7767 (tmtp) REVERT: I 7 LEU cc_start: 0.8387 (mt) cc_final: 0.8112 (mt) REVERT: I 10 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7792 (p0) REVERT: I 16 GLU cc_start: 0.6146 (tm-30) cc_final: 0.5726 (tm-30) REVERT: I 35 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7880 (mtp85) REVERT: I 56 MET cc_start: 0.8114 (mmm) cc_final: 0.7856 (mmp) REVERT: I 81 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6937 (mt-10) REVERT: I 111 PHE cc_start: 0.8391 (t80) cc_final: 0.8140 (t80) REVERT: I 115 SER cc_start: 0.8208 (p) cc_final: 0.7951 (t) REVERT: I 151 LYS cc_start: 0.7971 (tttm) cc_final: 0.6813 (ttmm) REVERT: I 155 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: I 290 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8041 (mtt180) REVERT: I 311 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6387 (mm-30) REVERT: I 390 SER cc_start: 0.8049 (m) cc_final: 0.7726 (t) REVERT: J 87 VAL cc_start: 0.8472 (t) cc_final: 0.8261 (t) REVERT: J 125 ASP cc_start: 0.6461 (t0) cc_final: 0.6039 (t0) REVERT: J 128 GLU cc_start: 0.6978 (tp30) cc_final: 0.6711 (tp30) outliers start: 205 outliers final: 118 residues processed: 998 average time/residue: 1.4296 time to fit residues: 1650.5149 Evaluate side-chains 1028 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 889 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 625 SER Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 680 SER Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain G residue 272 HIS Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 6.9990 chunk 193 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 140 optimal weight: 0.0870 chunk 290 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 0.8980 chunk 305 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 556 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN F 175 GLN F 562 ASN ** F 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28762 Z= 0.170 Angle : 0.586 12.191 39014 Z= 0.291 Chirality : 0.044 0.164 4358 Planarity : 0.005 0.053 4988 Dihedral : 8.800 175.175 4084 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 6.48 % Allowed : 27.57 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3554 helix: -0.00 (0.14), residues: 1402 sheet: -0.85 (0.29), residues: 342 loop : -1.97 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 326 HIS 0.006 0.001 HIS B 116 PHE 0.025 0.001 PHE G 446 TYR 0.013 0.001 TYR I 315 ARG 0.007 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 898 time to evaluate : 3.428 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7897 (mtm) cc_final: 0.7671 (mtm) REVERT: A 69 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7764 (mm-40) REVERT: A 86 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7337 (ttp-170) REVERT: A 120 MET cc_start: 0.7917 (ttp) cc_final: 0.7566 (ttt) REVERT: A 133 GLU cc_start: 0.7083 (pt0) cc_final: 0.6848 (pt0) REVERT: A 309 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7893 (ttmt) REVERT: A 322 SER cc_start: 0.7962 (p) cc_final: 0.7707 (t) REVERT: A 345 ILE cc_start: 0.8341 (mm) cc_final: 0.7956 (mm) REVERT: A 381 ASP cc_start: 0.7331 (m-30) cc_final: 0.6997 (m-30) REVERT: A 408 ARG cc_start: 0.7343 (mtt90) cc_final: 0.6954 (mtt90) REVERT: A 413 MET cc_start: 0.6534 (ptp) cc_final: 0.5912 (ptt) REVERT: A 429 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6548 (p0) REVERT: A 440 LYS cc_start: 0.7310 (tptt) cc_final: 0.7005 (tptt) REVERT: A 517 LYS cc_start: 0.7563 (pptt) cc_final: 0.7191 (pptt) REVERT: A 520 GLU cc_start: 0.6801 (mp0) cc_final: 0.6332 (mp0) REVERT: A 611 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8249 (pp) REVERT: A 636 ARG cc_start: 0.7143 (mmt90) cc_final: 0.6915 (mmt90) REVERT: A 655 MET cc_start: 0.8175 (mmp) cc_final: 0.7940 (mmm) REVERT: B 129 GLU cc_start: 0.7177 (tp30) cc_final: 0.6904 (tp30) REVERT: B 206 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6988 (ttm-80) REVERT: B 212 ASP cc_start: 0.7267 (p0) cc_final: 0.6782 (p0) REVERT: B 218 GLU cc_start: 0.6739 (tt0) cc_final: 0.6413 (tt0) REVERT: B 222 ILE cc_start: 0.8739 (mt) cc_final: 0.8521 (mp) REVERT: B 231 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6457 (mm-30) REVERT: B 249 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.7974 (pt) REVERT: B 271 PHE cc_start: 0.7904 (t80) cc_final: 0.7672 (t80) REVERT: B 316 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8206 (mmtm) REVERT: B 334 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8018 (tp) REVERT: B 356 LEU cc_start: 0.7778 (tp) cc_final: 0.7535 (tt) REVERT: B 387 ASN cc_start: 0.7481 (m-40) cc_final: 0.7231 (m-40) REVERT: B 396 ILE cc_start: 0.7669 (mm) cc_final: 0.7385 (mt) REVERT: B 404 LEU cc_start: 0.8174 (mm) cc_final: 0.7941 (mt) REVERT: B 521 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7150 (tp30) REVERT: C 10 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6512 (pm20) REVERT: C 11 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7839 (tmtp) REVERT: D 16 GLU cc_start: 0.5951 (tm-30) cc_final: 0.5499 (tm-30) REVERT: D 204 LEU cc_start: 0.8164 (tp) cc_final: 0.7951 (tt) REVERT: D 207 ASP cc_start: 0.7043 (m-30) cc_final: 0.6791 (m-30) REVERT: D 269 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6657 (mm-30) REVERT: D 307 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6195 (tm-30) REVERT: D 311 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6258 (mm-30) REVERT: D 390 SER cc_start: 0.8045 (m) cc_final: 0.7690 (t) REVERT: E 20 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.8070 (t) REVERT: E 65 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: F 5 THR cc_start: 0.8371 (p) cc_final: 0.8127 (t) REVERT: F 60 MET cc_start: 0.8064 (mtm) cc_final: 0.7829 (mtm) REVERT: F 90 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7292 (mm-30) REVERT: F 119 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7027 (mt-10) REVERT: F 120 MET cc_start: 0.7781 (ttp) cc_final: 0.7446 (ttt) REVERT: F 133 GLU cc_start: 0.6973 (pt0) cc_final: 0.6704 (pt0) REVERT: F 138 ASP cc_start: 0.7645 (t0) cc_final: 0.7373 (t0) REVERT: F 156 ARG cc_start: 0.7257 (mmt90) cc_final: 0.6917 (mmt90) REVERT: F 309 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7576 (ttmt) REVERT: F 322 SER cc_start: 0.8009 (p) cc_final: 0.7733 (t) REVERT: F 345 ILE cc_start: 0.8295 (mm) cc_final: 0.7926 (mm) REVERT: F 383 ILE cc_start: 0.8082 (mt) cc_final: 0.7813 (mp) REVERT: F 385 THR cc_start: 0.7963 (m) cc_final: 0.7300 (t) REVERT: F 411 LYS cc_start: 0.7881 (mtpp) cc_final: 0.7530 (mtpp) REVERT: F 429 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6719 (p0) REVERT: F 517 LYS cc_start: 0.7350 (pptt) cc_final: 0.7027 (pptt) REVERT: F 585 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6710 (mm-30) REVERT: F 594 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7342 (m) REVERT: F 611 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8414 (pp) REVERT: F 623 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6942 (mt-10) REVERT: F 636 ARG cc_start: 0.7139 (mmt90) cc_final: 0.6833 (mtt90) REVERT: F 638 LEU cc_start: 0.8553 (mt) cc_final: 0.8253 (mp) REVERT: F 655 MET cc_start: 0.8190 (mmp) cc_final: 0.7921 (mmm) REVERT: G 179 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7252 (tm-30) REVERT: G 183 LYS cc_start: 0.8145 (mttm) cc_final: 0.7872 (mttm) REVERT: G 222 ILE cc_start: 0.8751 (mt) cc_final: 0.8508 (mp) REVERT: G 313 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7550 (mp) REVERT: G 487 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7858 (mtmt) REVERT: G 516 ARG cc_start: 0.7447 (ptm160) cc_final: 0.7228 (ptm160) REVERT: H 10 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: H 11 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7800 (tmtp) REVERT: I 16 GLU cc_start: 0.6088 (tm-30) cc_final: 0.5694 (tm-30) REVERT: I 56 MET cc_start: 0.8158 (mmm) cc_final: 0.7878 (mmp) REVERT: I 111 PHE cc_start: 0.8356 (t80) cc_final: 0.8121 (t80) REVERT: I 115 SER cc_start: 0.8185 (p) cc_final: 0.7941 (t) REVERT: I 151 LYS cc_start: 0.7946 (tttm) cc_final: 0.6879 (ttmm) REVERT: I 155 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: I 311 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6355 (mm-30) REVERT: I 390 SER cc_start: 0.8048 (m) cc_final: 0.7740 (t) REVERT: J 20 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8074 (t) REVERT: J 65 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6342 (mt-10) REVERT: J 87 VAL cc_start: 0.8444 (t) cc_final: 0.8239 (t) REVERT: J 125 ASP cc_start: 0.6477 (t0) cc_final: 0.6020 (t0) REVERT: J 128 GLU cc_start: 0.7000 (tp30) cc_final: 0.6748 (tp30) outliers start: 194 outliers final: 109 residues processed: 998 average time/residue: 1.4353 time to fit residues: 1655.6865 Evaluate side-chains 1029 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 900 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 625 SER Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 680 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain G residue 272 HIS Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 160 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 340 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 157 optimal weight: 0.0570 chunk 28 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 178 optimal weight: 0.3980 overall best weight: 1.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 556 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN F 652 HIS G 335 ASN ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28762 Z= 0.280 Angle : 0.624 12.417 39014 Z= 0.309 Chirality : 0.046 0.177 4358 Planarity : 0.005 0.056 4988 Dihedral : 8.770 174.960 4073 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 6.51 % Allowed : 28.14 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3554 helix: 0.10 (0.14), residues: 1394 sheet: -0.80 (0.27), residues: 406 loop : -1.93 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.005 0.001 HIS F 165 PHE 0.029 0.002 PHE B 446 TYR 0.014 0.001 TYR I 315 ARG 0.008 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 910 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7931 (mtm) cc_final: 0.7694 (mtm) REVERT: A 86 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7434 (ttp-170) REVERT: A 120 MET cc_start: 0.7925 (ttp) cc_final: 0.7576 (ttt) REVERT: A 309 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7962 (ttmt) REVERT: A 322 SER cc_start: 0.7974 (p) cc_final: 0.7733 (t) REVERT: A 345 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7958 (mm) REVERT: A 381 ASP cc_start: 0.7369 (m-30) cc_final: 0.7035 (m-30) REVERT: A 408 ARG cc_start: 0.7339 (mtt90) cc_final: 0.6977 (mtt90) REVERT: A 440 LYS cc_start: 0.7343 (tptt) cc_final: 0.7050 (tptt) REVERT: A 517 LYS cc_start: 0.7599 (pptt) cc_final: 0.7215 (pptt) REVERT: A 520 GLU cc_start: 0.6808 (mp0) cc_final: 0.6323 (mp0) REVERT: A 611 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8251 (pp) REVERT: A 655 MET cc_start: 0.8172 (mmp) cc_final: 0.7966 (mmm) REVERT: B 129 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.7010 (tp30) REVERT: B 212 ASP cc_start: 0.7304 (p0) cc_final: 0.6446 (p0) REVERT: B 218 GLU cc_start: 0.6796 (tt0) cc_final: 0.6496 (tt0) REVERT: B 222 ILE cc_start: 0.8724 (mt) cc_final: 0.8503 (mp) REVERT: B 231 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6484 (mm-30) REVERT: B 249 ILE cc_start: 0.8528 (pp) cc_final: 0.8250 (pt) REVERT: B 271 PHE cc_start: 0.7931 (t80) cc_final: 0.7715 (t80) REVERT: B 316 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8276 (mmtm) REVERT: B 319 ASN cc_start: 0.8084 (t0) cc_final: 0.7741 (t0) REVERT: B 334 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8040 (tp) REVERT: B 349 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7985 (mmtt) REVERT: B 356 LEU cc_start: 0.7800 (tp) cc_final: 0.7555 (tt) REVERT: B 361 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.6770 (m) REVERT: B 387 ASN cc_start: 0.7555 (m-40) cc_final: 0.7271 (m-40) REVERT: B 396 ILE cc_start: 0.7774 (mm) cc_final: 0.7543 (mm) REVERT: B 404 LEU cc_start: 0.8285 (mm) cc_final: 0.8030 (mt) REVERT: B 424 ILE cc_start: 0.8305 (tp) cc_final: 0.8033 (pp) REVERT: B 453 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6838 (mm-30) REVERT: B 471 MET cc_start: 0.7654 (mtt) cc_final: 0.7451 (mtm) REVERT: C 10 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: C 11 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7762 (tmtp) REVERT: D 16 GLU cc_start: 0.6023 (tm-30) cc_final: 0.5560 (tm-30) REVERT: D 197 ILE cc_start: 0.8225 (mt) cc_final: 0.7948 (mp) REVERT: D 204 LEU cc_start: 0.8162 (tp) cc_final: 0.7947 (tt) REVERT: D 207 ASP cc_start: 0.7028 (m-30) cc_final: 0.6782 (m-30) REVERT: D 311 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6302 (mm-30) REVERT: D 390 SER cc_start: 0.8069 (m) cc_final: 0.7709 (t) REVERT: E 20 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.8111 (t) REVERT: E 65 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: F 5 THR cc_start: 0.8302 (p) cc_final: 0.7732 (m) REVERT: F 60 MET cc_start: 0.8101 (mtm) cc_final: 0.7863 (mtm) REVERT: F 90 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7354 (mm-30) REVERT: F 120 MET cc_start: 0.7783 (ttp) cc_final: 0.7458 (ttt) REVERT: F 133 GLU cc_start: 0.6983 (pt0) cc_final: 0.6695 (pt0) REVERT: F 138 ASP cc_start: 0.7677 (t0) cc_final: 0.7425 (t0) REVERT: F 156 ARG cc_start: 0.7266 (mmt90) cc_final: 0.6925 (mmt90) REVERT: F 309 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7553 (ttmt) REVERT: F 322 SER cc_start: 0.7967 (p) cc_final: 0.7685 (t) REVERT: F 345 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7859 (mm) REVERT: F 383 ILE cc_start: 0.8120 (mt) cc_final: 0.7892 (mp) REVERT: F 385 THR cc_start: 0.7961 (m) cc_final: 0.7335 (t) REVERT: F 411 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7585 (mtpp) REVERT: F 501 LEU cc_start: 0.7442 (tm) cc_final: 0.7242 (tt) REVERT: F 517 LYS cc_start: 0.7394 (pptt) cc_final: 0.7062 (pptt) REVERT: F 585 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6688 (mm-30) REVERT: F 594 THR cc_start: 0.7832 (OUTLIER) cc_final: 0.7551 (m) REVERT: F 611 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8411 (pp) REVERT: F 623 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6998 (mt-10) REVERT: F 638 LEU cc_start: 0.8558 (mt) cc_final: 0.8237 (mp) REVERT: F 655 MET cc_start: 0.8149 (mmp) cc_final: 0.7881 (mmm) REVERT: G 174 THR cc_start: 0.7778 (p) cc_final: 0.7569 (m) REVERT: G 179 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7281 (tm-30) REVERT: G 183 LYS cc_start: 0.8164 (mttm) cc_final: 0.7902 (mttm) REVERT: G 212 ASP cc_start: 0.7520 (p0) cc_final: 0.6827 (p0) REVERT: G 222 ILE cc_start: 0.8743 (mt) cc_final: 0.8456 (mp) REVERT: G 313 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7777 (mp) REVERT: G 356 LEU cc_start: 0.8053 (tt) cc_final: 0.7845 (tt) REVERT: G 487 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7939 (mtmt) REVERT: G 531 CYS cc_start: 0.7054 (t) cc_final: 0.6653 (t) REVERT: H 10 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: H 11 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7767 (tmtp) REVERT: I 7 LEU cc_start: 0.8470 (mt) cc_final: 0.8142 (mp) REVERT: I 8 GLU cc_start: 0.6674 (mp0) cc_final: 0.6474 (mp0) REVERT: I 16 GLU cc_start: 0.6146 (tm-30) cc_final: 0.5754 (tm-30) REVERT: I 35 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7843 (mtp85) REVERT: I 56 MET cc_start: 0.8125 (mmm) cc_final: 0.7853 (mmp) REVERT: I 111 PHE cc_start: 0.8392 (t80) cc_final: 0.8168 (t80) REVERT: I 115 SER cc_start: 0.8187 (p) cc_final: 0.7945 (t) REVERT: I 151 LYS cc_start: 0.7987 (tttm) cc_final: 0.6861 (ttmm) REVERT: I 155 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: I 195 LYS cc_start: 0.7934 (mttt) cc_final: 0.7599 (mttt) REVERT: I 311 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6382 (mm-30) REVERT: I 346 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6681 (mt-10) REVERT: I 390 SER cc_start: 0.8056 (m) cc_final: 0.7737 (t) REVERT: J 64 GLU cc_start: 0.6788 (tm-30) cc_final: 0.6434 (tm-30) REVERT: J 65 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6459 (mt-10) REVERT: J 87 VAL cc_start: 0.8456 (t) cc_final: 0.8251 (t) REVERT: J 125 ASP cc_start: 0.6503 (t0) cc_final: 0.6035 (t0) REVERT: J 128 GLU cc_start: 0.7010 (tp30) cc_final: 0.6754 (tp30) outliers start: 195 outliers final: 119 residues processed: 999 average time/residue: 1.5103 time to fit residues: 1754.2153 Evaluate side-chains 1043 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 904 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 625 SER Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 272 HIS Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 248 optimal weight: 0.2980 chunk 192 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 339 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 262 GLN A 366 GLN A 556 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN I 298 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28762 Z= 0.304 Angle : 0.635 12.056 39014 Z= 0.315 Chirality : 0.047 0.174 4358 Planarity : 0.005 0.059 4988 Dihedral : 8.749 175.218 4069 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 6.07 % Allowed : 28.94 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.14), residues: 3554 helix: 0.12 (0.14), residues: 1392 sheet: -0.81 (0.27), residues: 410 loop : -1.89 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 168 HIS 0.005 0.001 HIS F 165 PHE 0.027 0.002 PHE G 446 TYR 0.013 0.001 TYR A 102 ARG 0.007 0.001 ARG I 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 914 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7933 (mtm) cc_final: 0.7691 (mtm) REVERT: A 120 MET cc_start: 0.7931 (ttp) cc_final: 0.7618 (ttt) REVERT: A 309 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7971 (ttmt) REVERT: A 322 SER cc_start: 0.7990 (p) cc_final: 0.7716 (t) REVERT: A 345 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7944 (mm) REVERT: A 381 ASP cc_start: 0.7352 (m-30) cc_final: 0.7027 (m-30) REVERT: A 408 ARG cc_start: 0.7326 (mtt90) cc_final: 0.6978 (mtt90) REVERT: A 413 MET cc_start: 0.6560 (ptt) cc_final: 0.6313 (ptp) REVERT: A 440 LYS cc_start: 0.7411 (tptt) cc_final: 0.6825 (tptt) REVERT: A 517 LYS cc_start: 0.7613 (pptt) cc_final: 0.7234 (pptt) REVERT: A 520 GLU cc_start: 0.6825 (mp0) cc_final: 0.6339 (mp0) REVERT: A 611 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8243 (pp) REVERT: B 174 THR cc_start: 0.7628 (p) cc_final: 0.7390 (m) REVERT: B 206 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7200 (ttm-80) REVERT: B 212 ASP cc_start: 0.7299 (p0) cc_final: 0.6719 (p0) REVERT: B 218 GLU cc_start: 0.6793 (tt0) cc_final: 0.6490 (tt0) REVERT: B 222 ILE cc_start: 0.8694 (mt) cc_final: 0.8491 (mp) REVERT: B 231 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6468 (mm-30) REVERT: B 271 PHE cc_start: 0.7936 (t80) cc_final: 0.7733 (t80) REVERT: B 286 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6354 (tm-30) REVERT: B 287 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6462 (mt-10) REVERT: B 313 LEU cc_start: 0.8175 (mt) cc_final: 0.7822 (mp) REVERT: B 316 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8267 (mmtm) REVERT: B 319 ASN cc_start: 0.8086 (t0) cc_final: 0.7752 (t160) REVERT: B 334 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8073 (tp) REVERT: B 356 LEU cc_start: 0.7800 (tp) cc_final: 0.7550 (tt) REVERT: B 361 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.6860 (m) REVERT: B 367 GLU cc_start: 0.6627 (mt-10) cc_final: 0.6330 (tt0) REVERT: B 381 LEU cc_start: 0.8462 (tt) cc_final: 0.8169 (tm) REVERT: B 387 ASN cc_start: 0.7600 (m-40) cc_final: 0.7315 (m-40) REVERT: B 396 ILE cc_start: 0.7804 (mm) cc_final: 0.7535 (mm) REVERT: B 404 LEU cc_start: 0.8304 (mm) cc_final: 0.8072 (mt) REVERT: B 424 ILE cc_start: 0.8313 (tp) cc_final: 0.8041 (pp) REVERT: B 516 ARG cc_start: 0.7343 (ptm160) cc_final: 0.7135 (ptm160) REVERT: C 10 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6545 (pm20) REVERT: C 11 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7772 (tmtp) REVERT: D 16 GLU cc_start: 0.5979 (tm-30) cc_final: 0.5536 (tm-30) REVERT: D 115 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7926 (t) REVERT: D 204 LEU cc_start: 0.8183 (tp) cc_final: 0.7967 (tt) REVERT: D 207 ASP cc_start: 0.7029 (m-30) cc_final: 0.6781 (m-30) REVERT: D 311 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6280 (mm-30) REVERT: D 390 SER cc_start: 0.8069 (m) cc_final: 0.7674 (t) REVERT: E 20 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.8144 (t) REVERT: E 67 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6529 (mm-30) REVERT: F 5 THR cc_start: 0.8334 (p) cc_final: 0.8080 (m) REVERT: F 60 MET cc_start: 0.8100 (mtm) cc_final: 0.7880 (mtm) REVERT: F 90 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7318 (mm-30) REVERT: F 119 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7084 (mp0) REVERT: F 120 MET cc_start: 0.7805 (ttp) cc_final: 0.7457 (ttt) REVERT: F 133 GLU cc_start: 0.6981 (pt0) cc_final: 0.6690 (pt0) REVERT: F 138 ASP cc_start: 0.7680 (t0) cc_final: 0.7420 (t0) REVERT: F 156 ARG cc_start: 0.7275 (mmt90) cc_final: 0.6930 (mmt90) REVERT: F 175 GLN cc_start: 0.7775 (mm110) cc_final: 0.7552 (mm-40) REVERT: F 297 GLU cc_start: 0.7004 (tp30) cc_final: 0.6699 (tp30) REVERT: F 306 GLU cc_start: 0.6862 (tp30) cc_final: 0.6494 (tp30) REVERT: F 309 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7749 (ttmt) REVERT: F 322 SER cc_start: 0.7946 (p) cc_final: 0.7660 (t) REVERT: F 345 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7912 (mm) REVERT: F 383 ILE cc_start: 0.8128 (mt) cc_final: 0.7915 (mp) REVERT: F 385 THR cc_start: 0.7937 (m) cc_final: 0.7326 (t) REVERT: F 411 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7599 (mtpp) REVERT: F 517 LYS cc_start: 0.7421 (pptt) cc_final: 0.7089 (pptt) REVERT: F 568 GLU cc_start: 0.7258 (mp0) cc_final: 0.7019 (mp0) REVERT: F 585 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6682 (mm-30) REVERT: F 594 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7596 (m) REVERT: F 623 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6991 (mt-10) REVERT: F 638 LEU cc_start: 0.8571 (mt) cc_final: 0.8244 (mp) REVERT: F 655 MET cc_start: 0.8187 (mmp) cc_final: 0.7945 (mmm) REVERT: G 118 ILE cc_start: 0.8257 (mt) cc_final: 0.8050 (mp) REVERT: G 179 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7274 (tm-30) REVERT: G 183 LYS cc_start: 0.8175 (mttm) cc_final: 0.7895 (mttm) REVERT: G 189 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7731 (mttm) REVERT: G 218 GLU cc_start: 0.6845 (tt0) cc_final: 0.6516 (tt0) REVERT: G 222 ILE cc_start: 0.8718 (mt) cc_final: 0.8476 (mp) REVERT: G 313 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7737 (mp) REVERT: G 487 LYS cc_start: 0.8273 (mtmm) cc_final: 0.8017 (mtmt) REVERT: H 10 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: H 11 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7695 (tmtp) REVERT: I 7 LEU cc_start: 0.8455 (mt) cc_final: 0.8002 (mp) REVERT: I 16 GLU cc_start: 0.6102 (tm-30) cc_final: 0.5723 (tm-30) REVERT: I 35 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7823 (mtp85) REVERT: I 56 MET cc_start: 0.8125 (mmm) cc_final: 0.7857 (mmp) REVERT: I 115 SER cc_start: 0.8185 (p) cc_final: 0.7914 (t) REVERT: I 151 LYS cc_start: 0.8006 (tttm) cc_final: 0.6819 (ttmm) REVERT: I 155 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6280 (mp0) REVERT: I 311 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6376 (mm-30) REVERT: I 390 SER cc_start: 0.8071 (m) cc_final: 0.7765 (t) REVERT: J 65 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6460 (mt-10) REVERT: J 87 VAL cc_start: 0.8451 (t) cc_final: 0.8242 (t) REVERT: J 125 ASP cc_start: 0.6501 (t0) cc_final: 0.6033 (t0) REVERT: J 128 GLU cc_start: 0.7011 (tp30) cc_final: 0.6761 (tp30) outliers start: 182 outliers final: 127 residues processed: 999 average time/residue: 1.4697 time to fit residues: 1691.3290 Evaluate side-chains 1054 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 908 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 625 SER Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain G residue 272 HIS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 0.0040 chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 262 GLN A 556 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN I 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28762 Z= 0.313 Angle : 0.659 13.419 39014 Z= 0.325 Chirality : 0.048 0.176 4358 Planarity : 0.005 0.060 4988 Dihedral : 8.708 175.693 4068 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 6.24 % Allowed : 29.01 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3554 helix: 0.14 (0.14), residues: 1388 sheet: -0.83 (0.27), residues: 410 loop : -1.88 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 168 HIS 0.005 0.001 HIS F 165 PHE 0.032 0.002 PHE B 446 TYR 0.015 0.001 TYR A 37 ARG 0.007 0.001 ARG I 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 916 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8132 (p) cc_final: 0.7895 (t) REVERT: A 60 MET cc_start: 0.7932 (mtm) cc_final: 0.7708 (mtm) REVERT: A 120 MET cc_start: 0.7934 (ttp) cc_final: 0.7631 (ttt) REVERT: A 138 ASP cc_start: 0.7661 (t0) cc_final: 0.7432 (t0) REVERT: A 309 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7992 (ttmt) REVERT: A 322 SER cc_start: 0.7985 (p) cc_final: 0.7714 (t) REVERT: A 345 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7864 (mm) REVERT: A 381 ASP cc_start: 0.7360 (m-30) cc_final: 0.7039 (m-30) REVERT: A 408 ARG cc_start: 0.7320 (mtt90) cc_final: 0.6988 (mtt90) REVERT: A 413 MET cc_start: 0.6533 (ptt) cc_final: 0.6283 (ptp) REVERT: A 440 LYS cc_start: 0.7446 (tptt) cc_final: 0.6886 (tptt) REVERT: A 517 LYS cc_start: 0.7621 (pptt) cc_final: 0.7244 (pptt) REVERT: A 520 GLU cc_start: 0.6843 (mp0) cc_final: 0.6343 (mp0) REVERT: A 611 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8233 (pp) REVERT: B 129 GLU cc_start: 0.7252 (tp30) cc_final: 0.7026 (mp0) REVERT: B 183 LYS cc_start: 0.8286 (mttm) cc_final: 0.8064 (mttt) REVERT: B 205 ASP cc_start: 0.6647 (t0) cc_final: 0.6378 (t0) REVERT: B 212 ASP cc_start: 0.7299 (p0) cc_final: 0.6778 (p0) REVERT: B 218 GLU cc_start: 0.6782 (tt0) cc_final: 0.6489 (tt0) REVERT: B 222 ILE cc_start: 0.8692 (mt) cc_final: 0.8488 (mp) REVERT: B 231 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6488 (mm-30) REVERT: B 249 ILE cc_start: 0.8615 (pp) cc_final: 0.8315 (pt) REVERT: B 313 LEU cc_start: 0.8206 (mt) cc_final: 0.7846 (mp) REVERT: B 319 ASN cc_start: 0.8090 (t0) cc_final: 0.7725 (t0) REVERT: B 334 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8092 (tp) REVERT: B 356 LEU cc_start: 0.7850 (tp) cc_final: 0.7608 (tt) REVERT: B 361 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.6836 (m) REVERT: B 387 ASN cc_start: 0.7643 (m-40) cc_final: 0.7366 (m-40) REVERT: B 396 ILE cc_start: 0.7935 (mm) cc_final: 0.7656 (mm) REVERT: B 404 LEU cc_start: 0.8296 (mm) cc_final: 0.8074 (mt) REVERT: B 424 ILE cc_start: 0.8324 (tp) cc_final: 0.8045 (pp) REVERT: C 10 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6534 (pm20) REVERT: C 11 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7862 (tmtp) REVERT: D 16 GLU cc_start: 0.5948 (tm-30) cc_final: 0.5521 (tm-30) REVERT: D 115 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7897 (t) REVERT: D 197 ILE cc_start: 0.8236 (mt) cc_final: 0.7978 (mp) REVERT: D 204 LEU cc_start: 0.8172 (tp) cc_final: 0.7914 (tt) REVERT: D 207 ASP cc_start: 0.7032 (m-30) cc_final: 0.6688 (m-30) REVERT: D 290 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8321 (mtt180) REVERT: D 311 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6280 (mm-30) REVERT: D 315 TYR cc_start: 0.8391 (t80) cc_final: 0.8070 (t80) REVERT: D 390 SER cc_start: 0.8067 (m) cc_final: 0.7661 (t) REVERT: E 20 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8163 (t) REVERT: E 65 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6311 (mt-10) REVERT: E 67 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6490 (mm-30) REVERT: F 5 THR cc_start: 0.8318 (p) cc_final: 0.8084 (m) REVERT: F 60 MET cc_start: 0.8115 (mtm) cc_final: 0.7905 (mtm) REVERT: F 90 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7371 (mm-30) REVERT: F 120 MET cc_start: 0.7811 (ttp) cc_final: 0.7502 (ttt) REVERT: F 133 GLU cc_start: 0.6975 (pt0) cc_final: 0.6678 (pt0) REVERT: F 138 ASP cc_start: 0.7680 (t0) cc_final: 0.7437 (t0) REVERT: F 156 ARG cc_start: 0.7276 (mmt90) cc_final: 0.6919 (mmt90) REVERT: F 175 GLN cc_start: 0.7839 (mm110) cc_final: 0.7544 (mm110) REVERT: F 306 GLU cc_start: 0.6879 (tp30) cc_final: 0.6517 (tp30) REVERT: F 309 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7774 (ttmt) REVERT: F 322 SER cc_start: 0.7941 (p) cc_final: 0.7644 (t) REVERT: F 328 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7369 (mt-10) REVERT: F 345 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7874 (mm) REVERT: F 383 ILE cc_start: 0.8142 (mt) cc_final: 0.7931 (mp) REVERT: F 385 THR cc_start: 0.7883 (m) cc_final: 0.7325 (t) REVERT: F 411 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7625 (mtpp) REVERT: F 447 GLU cc_start: 0.6645 (pt0) cc_final: 0.6398 (mt-10) REVERT: F 517 LYS cc_start: 0.7452 (pptt) cc_final: 0.7119 (pptt) REVERT: F 585 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6684 (mm-30) REVERT: F 594 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7650 (m) REVERT: F 623 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6994 (mt-10) REVERT: F 638 LEU cc_start: 0.8562 (mt) cc_final: 0.8224 (mp) REVERT: F 680 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7365 (p) REVERT: G 118 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8078 (mp) REVERT: G 179 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7273 (tm-30) REVERT: G 183 LYS cc_start: 0.8206 (mttm) cc_final: 0.7906 (mttm) REVERT: G 189 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7724 (mttm) REVERT: G 313 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7727 (mp) REVERT: G 356 LEU cc_start: 0.8119 (tt) cc_final: 0.7857 (tt) REVERT: G 487 LYS cc_start: 0.8280 (mtmm) cc_final: 0.8033 (mtmt) REVERT: G 494 MET cc_start: 0.7805 (tmm) cc_final: 0.7461 (tmm) REVERT: H 10 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6739 (pm20) REVERT: H 11 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7796 (tmtp) REVERT: I 16 GLU cc_start: 0.6121 (tm-30) cc_final: 0.5747 (tm-30) REVERT: I 35 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7842 (mtp85) REVERT: I 56 MET cc_start: 0.8118 (mmm) cc_final: 0.7851 (mmp) REVERT: I 115 SER cc_start: 0.8168 (p) cc_final: 0.7925 (t) REVERT: I 151 LYS cc_start: 0.8011 (tttm) cc_final: 0.6906 (ttmm) REVERT: I 155 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: I 204 LEU cc_start: 0.8151 (tp) cc_final: 0.7908 (tt) REVERT: I 311 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6350 (mm-30) REVERT: I 390 SER cc_start: 0.8078 (m) cc_final: 0.7771 (t) REVERT: J 65 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6438 (mt-10) REVERT: J 87 VAL cc_start: 0.8446 (t) cc_final: 0.8238 (t) REVERT: J 125 ASP cc_start: 0.6549 (t0) cc_final: 0.6096 (t0) REVERT: J 128 GLU cc_start: 0.7012 (tp30) cc_final: 0.6761 (tp30) outliers start: 187 outliers final: 134 residues processed: 1003 average time/residue: 1.4518 time to fit residues: 1680.4138 Evaluate side-chains 1063 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 908 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 625 SER Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 680 SER Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain G residue 272 HIS Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 0.9980 chunk 325 optimal weight: 0.9980 chunk 296 optimal weight: 0.4980 chunk 316 optimal weight: 1.9990 chunk 324 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 248 optimal weight: 0.0870 chunk 97 optimal weight: 6.9990 chunk 285 optimal weight: 0.9980 chunk 299 optimal weight: 0.2980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 262 GLN A 556 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN F 366 GLN I 102 GLN ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 397 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28762 Z= 0.175 Angle : 0.629 17.171 39014 Z= 0.306 Chirality : 0.043 0.148 4358 Planarity : 0.005 0.059 4988 Dihedral : 8.501 175.906 4068 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 5.01 % Allowed : 30.41 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3554 helix: 0.31 (0.14), residues: 1396 sheet: -0.55 (0.29), residues: 358 loop : -1.79 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 174 HIS 0.005 0.001 HIS A 165 PHE 0.019 0.001 PHE G 446 TYR 0.014 0.001 TYR A 37 ARG 0.008 0.000 ARG F 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 900 time to evaluate : 3.201 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7912 (mtm) cc_final: 0.7687 (mtm) REVERT: A 120 MET cc_start: 0.7964 (ttp) cc_final: 0.7645 (ttt) REVERT: A 309 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7931 (ttmt) REVERT: A 322 SER cc_start: 0.7974 (p) cc_final: 0.7719 (t) REVERT: A 345 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7963 (mm) REVERT: A 381 ASP cc_start: 0.7337 (m-30) cc_final: 0.7032 (m-30) REVERT: A 408 ARG cc_start: 0.7309 (mtt90) cc_final: 0.7005 (mtt90) REVERT: A 413 MET cc_start: 0.6517 (ptt) cc_final: 0.6276 (ptp) REVERT: A 440 LYS cc_start: 0.7386 (tptt) cc_final: 0.7111 (tptt) REVERT: A 517 LYS cc_start: 0.7617 (pptt) cc_final: 0.7241 (pptt) REVERT: A 520 GLU cc_start: 0.6825 (mp0) cc_final: 0.6339 (mp0) REVERT: A 611 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8249 (pp) REVERT: A 668 ARG cc_start: 0.7000 (mmm160) cc_final: 0.6638 (mmm160) REVERT: A 680 SER cc_start: 0.7837 (OUTLIER) cc_final: 0.7471 (p) REVERT: B 129 GLU cc_start: 0.7209 (tp30) cc_final: 0.7008 (mp0) REVERT: B 212 ASP cc_start: 0.7208 (p0) cc_final: 0.6740 (p0) REVERT: B 218 GLU cc_start: 0.6721 (tt0) cc_final: 0.6434 (tt0) REVERT: B 222 ILE cc_start: 0.8659 (mt) cc_final: 0.8444 (mp) REVERT: B 231 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6453 (mm-30) REVERT: B 249 ILE cc_start: 0.8617 (pp) cc_final: 0.8343 (pt) REVERT: B 319 ASN cc_start: 0.8020 (t0) cc_final: 0.7710 (t160) REVERT: B 334 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8058 (tp) REVERT: B 356 LEU cc_start: 0.7826 (tp) cc_final: 0.7572 (tt) REVERT: B 361 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.6684 (m) REVERT: C 10 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6511 (pm20) REVERT: C 11 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7900 (tmtp) REVERT: C 62 VAL cc_start: 0.8264 (t) cc_final: 0.8022 (t) REVERT: D 207 ASP cc_start: 0.7048 (m-30) cc_final: 0.6784 (m-30) REVERT: D 311 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6193 (mm-30) REVERT: D 315 TYR cc_start: 0.8386 (t80) cc_final: 0.8058 (t80) REVERT: D 346 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6768 (mt-10) REVERT: D 390 SER cc_start: 0.8040 (m) cc_final: 0.7680 (t) REVERT: E 44 ASP cc_start: 0.6658 (m-30) cc_final: 0.6413 (m-30) REVERT: E 65 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6284 (mt-10) REVERT: F 5 THR cc_start: 0.8355 (p) cc_final: 0.8140 (m) REVERT: F 60 MET cc_start: 0.8072 (mtm) cc_final: 0.7863 (mtm) REVERT: F 90 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7339 (mm-30) REVERT: F 120 MET cc_start: 0.7820 (ttp) cc_final: 0.7496 (ttt) REVERT: F 133 GLU cc_start: 0.6975 (pt0) cc_final: 0.6700 (pt0) REVERT: F 138 ASP cc_start: 0.7668 (t0) cc_final: 0.7411 (t0) REVERT: F 156 ARG cc_start: 0.7221 (mmt90) cc_final: 0.6849 (mmt90) REVERT: F 175 GLN cc_start: 0.7800 (mm110) cc_final: 0.7473 (mm110) REVERT: F 227 SER cc_start: 0.8603 (p) cc_final: 0.8367 (t) REVERT: F 306 GLU cc_start: 0.6886 (tp30) cc_final: 0.6498 (tp30) REVERT: F 309 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7718 (ttmt) REVERT: F 322 SER cc_start: 0.7980 (p) cc_final: 0.7695 (t) REVERT: F 345 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7952 (mm) REVERT: F 383 ILE cc_start: 0.8148 (mt) cc_final: 0.7933 (mp) REVERT: F 411 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7598 (mtpp) REVERT: F 447 GLU cc_start: 0.6690 (pt0) cc_final: 0.6401 (mt-10) REVERT: F 517 LYS cc_start: 0.7477 (pptt) cc_final: 0.7148 (pptt) REVERT: F 580 MET cc_start: 0.8080 (mmm) cc_final: 0.7856 (mmp) REVERT: F 611 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8426 (pp) REVERT: F 623 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6992 (mt-10) REVERT: F 638 LEU cc_start: 0.8556 (mt) cc_final: 0.8279 (mp) REVERT: F 680 SER cc_start: 0.7707 (OUTLIER) cc_final: 0.7342 (p) REVERT: G 118 ILE cc_start: 0.8278 (mt) cc_final: 0.8065 (mp) REVERT: G 158 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6496 (pp20) REVERT: G 179 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7259 (tm-30) REVERT: G 183 LYS cc_start: 0.8106 (mttm) cc_final: 0.7821 (mttm) REVERT: G 218 GLU cc_start: 0.6674 (tt0) cc_final: 0.6316 (tt0) REVERT: G 222 ILE cc_start: 0.8768 (mt) cc_final: 0.8517 (mp) REVERT: G 356 LEU cc_start: 0.8110 (tt) cc_final: 0.7843 (tt) REVERT: G 487 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7868 (mtmt) REVERT: G 494 MET cc_start: 0.7731 (tmm) cc_final: 0.7427 (tmm) REVERT: H 10 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6736 (pm20) REVERT: H 11 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7832 (tmtp) REVERT: I 16 GLU cc_start: 0.6000 (tm-30) cc_final: 0.5607 (tm-30) REVERT: I 35 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7749 (mtp85) REVERT: I 56 MET cc_start: 0.8153 (mmm) cc_final: 0.7893 (mmp) REVERT: I 115 SER cc_start: 0.8134 (p) cc_final: 0.7892 (t) REVERT: I 151 LYS cc_start: 0.7968 (tttm) cc_final: 0.6814 (ttmm) REVERT: I 155 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: I 195 LYS cc_start: 0.7794 (mttt) cc_final: 0.7532 (mttt) REVERT: I 311 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6302 (mm-30) REVERT: I 346 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6559 (mt-10) REVERT: I 390 SER cc_start: 0.8053 (m) cc_final: 0.7757 (t) REVERT: J 67 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6335 (mm-30) REVERT: J 87 VAL cc_start: 0.8426 (t) cc_final: 0.8222 (t) REVERT: J 125 ASP cc_start: 0.6529 (t0) cc_final: 0.6089 (t0) REVERT: J 128 GLU cc_start: 0.7036 (tp30) cc_final: 0.6771 (tp30) outliers start: 150 outliers final: 95 residues processed: 970 average time/residue: 1.4642 time to fit residues: 1635.3715 Evaluate side-chains 990 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 879 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 680 SER Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 160 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 334 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 232 optimal weight: 0.3980 chunk 350 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 262 GLN A 414 ASN A 556 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 397 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28762 Z= 0.261 Angle : 0.659 16.412 39014 Z= 0.321 Chirality : 0.046 0.170 4358 Planarity : 0.005 0.059 4988 Dihedral : 8.457 176.115 4062 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.34 % Allowed : 31.51 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3554 helix: 0.31 (0.14), residues: 1390 sheet: -0.61 (0.27), residues: 398 loop : -1.75 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 174 HIS 0.005 0.001 HIS A 165 PHE 0.030 0.002 PHE G 271 TYR 0.015 0.001 TYR A 37 ARG 0.009 0.000 ARG F 688 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 896 time to evaluate : 3.248 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7936 (mtm) cc_final: 0.7712 (mtm) REVERT: A 120 MET cc_start: 0.7961 (ttp) cc_final: 0.7673 (ttt) REVERT: A 185 ARG cc_start: 0.5995 (mpt-90) cc_final: 0.5667 (mpt-90) REVERT: A 309 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7951 (ttmt) REVERT: A 322 SER cc_start: 0.7971 (p) cc_final: 0.7733 (t) REVERT: A 345 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7855 (mm) REVERT: A 381 ASP cc_start: 0.7361 (m-30) cc_final: 0.7055 (m-30) REVERT: A 408 ARG cc_start: 0.7306 (mtt90) cc_final: 0.6996 (mtt90) REVERT: A 413 MET cc_start: 0.6534 (ptt) cc_final: 0.6306 (ptp) REVERT: A 440 LYS cc_start: 0.7439 (tptt) cc_final: 0.7157 (tptt) REVERT: A 517 LYS cc_start: 0.7610 (pptt) cc_final: 0.7239 (pptt) REVERT: A 520 GLU cc_start: 0.6841 (mp0) cc_final: 0.6313 (mp0) REVERT: A 611 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8260 (pp) REVERT: A 668 ARG cc_start: 0.7011 (mmm160) cc_final: 0.6646 (mmm160) REVERT: B 129 GLU cc_start: 0.7212 (tp30) cc_final: 0.7007 (mp0) REVERT: B 183 LYS cc_start: 0.8263 (mttm) cc_final: 0.8044 (mttt) REVERT: B 212 ASP cc_start: 0.7257 (p0) cc_final: 0.6420 (p0) REVERT: B 218 GLU cc_start: 0.6754 (tt0) cc_final: 0.6459 (tt0) REVERT: B 231 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6524 (mm-30) REVERT: B 249 ILE cc_start: 0.8628 (pp) cc_final: 0.8369 (pt) REVERT: B 313 LEU cc_start: 0.8168 (mt) cc_final: 0.7814 (mp) REVERT: B 319 ASN cc_start: 0.8077 (t0) cc_final: 0.7749 (t160) REVERT: B 334 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8105 (tp) REVERT: B 356 LEU cc_start: 0.7844 (tp) cc_final: 0.7609 (tt) REVERT: B 361 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.6767 (m) REVERT: B 387 ASN cc_start: 0.7615 (m-40) cc_final: 0.7365 (m-40) REVERT: B 396 ILE cc_start: 0.7788 (mm) cc_final: 0.7566 (mm) REVERT: B 424 ILE cc_start: 0.8307 (tp) cc_final: 0.7998 (pp) REVERT: B 483 ASP cc_start: 0.6929 (m-30) cc_final: 0.6665 (m-30) REVERT: C 10 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6526 (pm20) REVERT: C 11 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7898 (tmtp) REVERT: D 56 MET cc_start: 0.8115 (mmm) cc_final: 0.7899 (mmp) REVERT: D 204 LEU cc_start: 0.8141 (tt) cc_final: 0.7934 (tp) REVERT: D 207 ASP cc_start: 0.6999 (m-30) cc_final: 0.6680 (m-30) REVERT: D 311 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6220 (mm-30) REVERT: D 315 TYR cc_start: 0.8390 (t80) cc_final: 0.8061 (t80) REVERT: D 390 SER cc_start: 0.8065 (m) cc_final: 0.7665 (t) REVERT: E 65 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6330 (mt-10) REVERT: F 60 MET cc_start: 0.8102 (mtm) cc_final: 0.7887 (mtm) REVERT: F 90 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7384 (mm-30) REVERT: F 120 MET cc_start: 0.7829 (ttp) cc_final: 0.7518 (ttt) REVERT: F 133 GLU cc_start: 0.6990 (pt0) cc_final: 0.6699 (pt0) REVERT: F 138 ASP cc_start: 0.7678 (t0) cc_final: 0.7426 (t0) REVERT: F 156 ARG cc_start: 0.7232 (mmt90) cc_final: 0.6855 (mmt90) REVERT: F 175 GLN cc_start: 0.7841 (mm110) cc_final: 0.7496 (mm110) REVERT: F 306 GLU cc_start: 0.6908 (tp30) cc_final: 0.6510 (tp30) REVERT: F 309 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7724 (ttmt) REVERT: F 322 SER cc_start: 0.7952 (p) cc_final: 0.7659 (t) REVERT: F 328 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7390 (mt-10) REVERT: F 345 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7858 (mm) REVERT: F 411 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7626 (mtpp) REVERT: F 447 GLU cc_start: 0.6703 (pt0) cc_final: 0.6426 (mt-10) REVERT: F 517 LYS cc_start: 0.7492 (pptt) cc_final: 0.7161 (pptt) REVERT: F 623 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7073 (mt-10) REVERT: F 638 LEU cc_start: 0.8559 (mt) cc_final: 0.8227 (mp) REVERT: G 118 ILE cc_start: 0.8288 (mt) cc_final: 0.8061 (mp) REVERT: G 158 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6488 (pp20) REVERT: G 179 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7272 (tm-30) REVERT: G 183 LYS cc_start: 0.8143 (mttm) cc_final: 0.7858 (mttm) REVERT: G 189 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7795 (mttm) REVERT: G 222 ILE cc_start: 0.8739 (mt) cc_final: 0.8483 (mp) REVERT: G 356 LEU cc_start: 0.8101 (tt) cc_final: 0.7851 (tt) REVERT: G 487 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7920 (mtmt) REVERT: G 494 MET cc_start: 0.7767 (tmm) cc_final: 0.7441 (tmm) REVERT: H 10 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6744 (pm20) REVERT: H 11 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7692 (tmtp) REVERT: I 16 GLU cc_start: 0.6065 (tm-30) cc_final: 0.5683 (tm-30) REVERT: I 35 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7813 (mtp85) REVERT: I 56 MET cc_start: 0.8140 (mmm) cc_final: 0.7864 (mmp) REVERT: I 115 SER cc_start: 0.8141 (p) cc_final: 0.7897 (t) REVERT: I 151 LYS cc_start: 0.8042 (tttm) cc_final: 0.6985 (ttmm) REVERT: I 155 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6312 (mp0) REVERT: I 311 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6315 (mm-30) REVERT: I 390 SER cc_start: 0.8068 (m) cc_final: 0.7767 (t) REVERT: J 87 VAL cc_start: 0.8447 (t) cc_final: 0.8245 (t) REVERT: J 125 ASP cc_start: 0.6535 (t0) cc_final: 0.6091 (t0) REVERT: J 128 GLU cc_start: 0.7048 (tp30) cc_final: 0.6785 (tp30) outliers start: 130 outliers final: 101 residues processed: 961 average time/residue: 1.5049 time to fit residues: 1670.8850 Evaluate side-chains 1012 residues out of total 2998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 897 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain F residue 585 GLU Chi-restraints excluded: chain F residue 595 ARG Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 625 SER Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 269 GLU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.4980 chunk 221 optimal weight: 5.9990 chunk 297 optimal weight: 0.6980 chunk 85 optimal weight: 0.0670 chunk 257 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 175 GLN A 262 GLN A 527 ASN A 556 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN F 527 ASN ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 397 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118573 restraints weight = 37615.130| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.84 r_work: 0.3289 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28762 Z= 0.263 Angle : 0.659 16.411 39014 Z= 0.322 Chirality : 0.046 0.168 4358 Planarity : 0.005 0.059 4988 Dihedral : 8.431 176.416 4060 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.27 % Allowed : 31.64 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3554 helix: 0.26 (0.14), residues: 1402 sheet: -0.57 (0.28), residues: 398 loop : -1.75 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 168 HIS 0.005 0.001 HIS A 165 PHE 0.028 0.002 PHE G 271 TYR 0.016 0.001 TYR G 140 ARG 0.008 0.000 ARG I 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20129.27 seconds wall clock time: 351 minutes 5.44 seconds (21065.44 seconds total)