Starting phenix.real_space_refine on Wed Feb 21 00:47:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/02_2024/7t2r_25633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/02_2024/7t2r_25633.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/02_2024/7t2r_25633_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/02_2024/7t2r_25633_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/02_2024/7t2r_25633_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/02_2024/7t2r_25633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/02_2024/7t2r_25633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/02_2024/7t2r_25633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/02_2024/7t2r_25633_updated.pdb" } resolution = 3.2 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= 0.003 sd= 0.039 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: 6 Type Number sf(0) Gaussians Fe 62 7.16 5 Ni 2 6.56 5 S 280 5.16 5 C 18476 2.51 5 N 5012 2.21 5 O 5384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A GLU 568": "OE1" <-> "OE2" 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 ARG 606": "NH1" <-> "NH2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 667": "OE1" <-> "OE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A ARG 683": "NH1" <-> "NH2" Residue "A ARG 688": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 197": "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 286": "OE1" <-> "OE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F GLU 160": "OE1" <-> "OE2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F ARG 218": "NH1" <-> "NH2" Residue "F GLU 251": "OE1" <-> "OE2" Residue "F GLU 257": "OE1" <-> "OE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F ARG 277": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F ARG 292": "NH1" <-> "NH2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "F GLU 314": "OE1" <-> "OE2" Residue "F ARG 354": "NH1" <-> "NH2" Residue "F GLU 365": "OE1" <-> "OE2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "F GLU 393": "OE1" <-> "OE2" Residue "F ARG 431": "NH1" <-> "NH2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "F GLU 447": "OE1" <-> "OE2" Residue "F GLU 482": "OE1" <-> "OE2" Residue "F GLU 495": "OE1" <-> "OE2" Residue "F ARG 555": "NH1" <-> "NH2" Residue "F GLU 568": "OE1" <-> "OE2" 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 657": "OE1" <-> "OE2" Residue "F GLU 667": "OE1" <-> "OE2" Residue "F GLU 670": "OE1" <-> "OE2" Residue "F GLU 675": "OE1" <-> "OE2" Residue "F GLU 676": "OE1" <-> "OE2" Residue "F ARG 683": "NH1" <-> "NH2" Residue "F ARG 688": "NH1" <-> "NH2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G GLU 197": "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 286": "OE1" <-> "OE2" Residue "G GLU 295": "OE1" <-> "OE2" Residue "G GLU 324": "OE1" <-> "OE2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G GLU 380": "OE1" <-> "OE2" Residue "G GLU 390": "OE1" <-> "OE2" Residue "G GLU 407": "OE1" <-> "OE2" Residue "G GLU 416": "OE1" <-> "OE2" Residue "G GLU 448": "OE1" <-> "OE2" Residue "G GLU 453": "OE1" <-> "OE2" Residue "G GLU 479": "OE1" <-> "OE2" Residue "G GLU 490": "OE1" <-> "OE2" Residue "G ARG 519": "NH1" <-> "NH2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H ARG 90": "NH1" <-> "NH2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "I GLU 8": "OE1" <-> "OE2" Residue "I GLU 16": "OE1" <-> "OE2" Residue "I GLU 33": "OE1" <-> "OE2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "I GLU 200": "OE1" <-> "OE2" Residue "I GLU 214": "OE1" <-> "OE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I GLU 241": "OE1" <-> "OE2" Residue "I ARG 248": "NH1" <-> "NH2" Residue "I ARG 250": "NH1" <-> "NH2" Residue "I GLU 266": "OE1" <-> "OE2" Residue "I GLU 307": "OE1" <-> "OE2" Residue "I GLU 311": "OE1" <-> "OE2" Residue "I GLU 317": "OE1" <-> "OE2" Residue "I GLU 320": "OE1" <-> "OE2" Residue "I ARG 360": "NH1" <-> "NH2" Residue "I GLU 365": "OE1" <-> "OE2" Residue "I GLU 435": "OE1" <-> "OE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "J GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29216 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5175 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 34, 'TRANS': 630} 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: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 403} Chain: "C" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1194 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143} Chain: "D" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3537 Classifications: {'peptide': 447} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 23, 'TRANS': 420} 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: 5175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5175 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 34, 'TRANS': 630} 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: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 403} Chain: "H" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1194 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143} Chain: "I" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3537 Classifications: {'peptide': 447} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 23, 'TRANS': 420} 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: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {'FES': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} 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: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {'FES': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} 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 31.656 68.766 59.286 1.00 49.30 S ATOM 349 SG CYS A 47 30.725 65.364 59.688 1.00 53.66 S ATOM 374 SG CYS A 50 25.923 67.067 58.436 1.00 50.06 S ATOM 477 SG CYS A 64 26.751 69.903 59.804 1.00 52.69 S ATOM 1573 SG CYS A 202 41.777 68.112 66.639 1.00 51.26 S ATOM 1165 SG CYS A 148 43.691 66.440 61.329 1.00 50.42 S ATOM 1212 SG CYS A 154 43.042 72.034 62.010 1.00 52.33 S ATOM 1186 SG CYS A 151 38.288 68.849 62.310 1.00 49.74 S ATOM 1532 SG CYS A 195 45.901 80.727 68.554 1.00 56.35 S ATOM 1244 SG CYS A 158 45.718 79.642 63.684 1.00 53.97 S ATOM 1547 SG CYS A 198 45.949 75.959 67.659 1.00 52.90 S ATOM 1511 SG CYS A 192 50.296 79.052 66.757 1.00 58.16 S ATOM 2033 SG CYS A 264 45.180 85.657 76.462 1.00 57.61 S ATOM 1803 SG CYS A 232 43.125 90.523 77.828 1.00 63.23 S ATOM 1782 SG CYS A 229 42.294 86.348 80.935 1.00 59.02 S ATOM 1825 SG CYS A 236 39.624 87.011 75.955 1.00 58.08 S ATOM 796 SG CYS A 103 43.524 61.017 71.838 1.00 55.92 S ATOM 835 SG CYS A 109 38.210 61.579 69.286 1.00 56.30 S ATOM 770 SG CYS A 100 40.177 55.762 70.732 1.00 55.21 S ATOM 7797 SG CYS B 458 34.077 65.327 49.619 1.00 58.98 S ATOM 8126 SG CYS B 501 32.977 66.957 44.616 1.00 65.59 S ATOM 7817 SG CYS B 461 36.809 61.754 46.340 1.00 57.54 S ATOM 7778 SG CYS B 455 37.882 68.135 47.536 1.00 66.88 S ATOM 8369 SG CYS B 531 42.120 39.232 34.911 1.00 85.72 S ATOM 7938 SG CYS B 476 44.640 42.774 39.765 1.00 76.36 S ATOM 9355 SG CYS C 123 44.897 61.987 25.004 1.00 92.37 S ATOM 9378 SG CYS C 127 43.846 60.417 23.882 1.00 95.29 S ATOM 9036 SG CYS C 82 48.002 59.174 27.938 1.00 92.20 S ATOM 9069 SG CYS C 87 48.041 56.538 26.217 1.00 90.23 S ATOM 10128 SG CYS D 67 53.843 44.588 86.132 1.00 52.51 S ATOM 13099 SG CYS D 444 53.801 40.086 85.845 1.00 55.10 S ATOM 13119 SG CYS D 447 55.596 43.381 83.505 1.00 53.34 S ATOM 10128 SG CYS D 67 53.843 44.588 86.132 1.00 52.51 S ATOM 13119 SG CYS D 447 55.596 43.381 83.505 1.00 53.34 S ATOM 13265 SG CYS E 17 42.766 43.157 77.105 1.00 55.34 S ATOM 13250 SG CYS E 14 47.756 44.526 78.463 1.00 52.33 S ATOM 14294 SG CYS E 149 44.430 48.364 76.267 1.00 55.61 S ATOM 13802 SG CYS E 85 46.309 45.316 72.705 1.00 54.62 S ATOM 14810 SG CYS F 36 114.462 65.004 59.286 1.00 49.30 S ATOM 14889 SG CYS F 47 115.393 68.406 59.688 1.00 53.66 S ATOM 14914 SG CYS F 50 120.195 66.703 58.436 1.00 50.06 S ATOM 15017 SG CYS F 64 119.367 63.867 59.804 1.00 52.69 S ATOM 16113 SG CYS F 202 104.341 65.658 66.639 1.00 51.26 S ATOM 15705 SG CYS F 148 102.427 67.330 61.329 1.00 50.42 S ATOM 15752 SG CYS F 154 103.076 61.736 62.010 1.00 52.33 S ATOM 15726 SG CYS F 151 107.830 64.921 62.310 1.00 49.74 S ATOM 16072 SG CYS F 195 100.217 53.043 68.554 1.00 56.35 S ATOM 15784 SG CYS F 158 100.400 54.128 63.684 1.00 53.97 S ATOM 16087 SG CYS F 198 100.169 57.811 67.659 1.00 52.90 S ATOM 16051 SG CYS F 192 95.822 54.718 66.757 1.00 58.16 S ATOM 16573 SG CYS F 264 100.938 48.113 76.462 1.00 57.61 S ATOM 16343 SG CYS F 232 102.993 43.247 77.828 1.00 63.23 S ATOM 16322 SG CYS F 229 103.824 47.422 80.935 1.00 59.02 S ATOM 16365 SG CYS F 236 106.494 46.759 75.955 1.00 58.08 S ATOM 15336 SG CYS F 103 102.594 72.753 71.838 1.00 55.92 S ATOM 15375 SG CYS F 109 107.908 72.191 69.286 1.00 56.30 S ATOM 15310 SG CYS F 100 105.941 78.008 70.732 1.00 55.21 S ATOM 22337 SG CYS G 458 112.041 68.443 49.619 1.00 58.98 S ATOM 22666 SG CYS G 501 113.141 66.813 44.616 1.00 65.59 S ATOM 22357 SG CYS G 461 109.309 72.016 46.340 1.00 57.54 S ATOM 22318 SG CYS G 455 108.236 65.635 47.536 1.00 66.88 S ATOM 22909 SG CYS G 531 103.998 94.538 34.911 1.00 85.72 S ATOM 22478 SG CYS G 476 101.478 90.996 39.765 1.00 76.36 S ATOM 23895 SG CYS H 123 101.221 71.783 25.004 1.00 92.37 S ATOM 23918 SG CYS H 127 102.272 73.353 23.882 1.00 95.29 S ATOM 23576 SG CYS H 82 98.116 74.596 27.938 1.00 92.20 S ATOM 23609 SG CYS H 87 98.077 77.232 26.217 1.00 90.23 S ATOM 24668 SG CYS I 67 92.275 89.182 86.132 1.00 52.51 S ATOM 27639 SG CYS I 444 92.317 93.684 85.845 1.00 55.10 S ATOM 27659 SG CYS I 447 90.522 90.389 83.505 1.00 53.34 S ATOM 24668 SG CYS I 67 92.275 89.182 86.132 1.00 52.51 S ATOM 27659 SG CYS I 447 90.522 90.389 83.505 1.00 53.34 S ATOM 27805 SG CYS J 17 103.352 90.613 77.105 1.00 55.34 S ATOM 27790 SG CYS J 14 98.362 89.244 78.463 1.00 52.33 S ATOM 28834 SG CYS J 149 101.688 85.406 76.267 1.00 55.61 S ATOM 28342 SG CYS J 85 99.809 88.454 72.705 1.00 54.62 S Time building chain proxies: 15.18, per 1000 atoms: 0.52 Number of scatterers: 29216 At special positions: 0 Unit cell: (148.176, 134.799, 125.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 2 28.00 Fe 62 26.01 S 280 16.00 O 5384 8.00 N 5012 7.00 C 18476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 629 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS F 629 " - pdb=" SG CYS F 674 " distance=2.03 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: 11.90 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 701 " pdb="FE1 FES A 701 " - pdb=" SG CYS A 36 " pdb="FE2 FES A 701 " - pdb=" SG CYS A 50 " pdb="FE2 FES A 701 " - pdb=" SG CYS A 64 " pdb="FE1 FES A 701 " - pdb=" SG CYS A 47 " pdb=" FES B 602 " pdb="FE2 FES B 602 " - pdb=" SG CYS B 476 " pdb="FE1 FES B 602 " - pdb=" SG CYS B 531 " pdb="FE1 FES B 602 " - pdb=" SG CYS B 438 " pdb="FE1 FES B 602 " - pdb=" NE2 HIS B 525 " pdb=" FES C 501 " pdb="FE1 FES C 501 " - pdb=" SG CYS C 123 " pdb="FE2 FES C 501 " - pdb=" SG CYS C 82 " pdb="FE1 FES C 501 " - pdb=" SG CYS C 127 " pdb="FE2 FES C 501 " - pdb=" SG CYS C 87 " pdb=" FES F 701 " pdb="FE1 FES F 701 " - pdb=" SG CYS F 36 " pdb="FE2 FES F 701 " - pdb=" SG CYS F 50 " pdb="FE2 FES F 701 " - pdb=" SG CYS F 64 " pdb="FE1 FES F 701 " - pdb=" SG CYS F 47 " pdb=" FES G 602 " pdb="FE2 FES G 602 " - pdb=" SG CYS G 476 " pdb="FE1 FES G 602 " - pdb=" SG CYS G 531 " pdb="FE1 FES G 602 " - pdb=" SG CYS G 438 " pdb="FE1 FES G 602 " - pdb=" NE2 HIS G 525 " pdb=" FES H 501 " pdb="FE1 FES H 501 " - pdb=" SG CYS H 123 " pdb="FE2 FES H 501 " - pdb=" SG CYS H 82 " pdb="FE1 FES H 501 " - pdb=" SG CYS H 127 " pdb="FE2 FES H 501 " - pdb=" SG CYS H 87 " pdb=" SF4 A 702 " pdb="FE4 SF4 A 702 " - pdb=" SG CYS A 151 " pdb="FE2 SF4 A 702 " - pdb=" SG CYS A 148 " pdb="FE3 SF4 A 702 " - pdb=" SG CYS A 154 " pdb="FE1 SF4 A 702 " - pdb=" SG CYS A 202 " pdb=" SF4 A 703 " pdb="FE1 SF4 A 703 " - pdb=" SG CYS A 195 " pdb="FE2 SF4 A 703 " - pdb=" SG CYS A 158 " pdb="FE3 SF4 A 703 " - pdb=" SG CYS A 198 " pdb="FE4 SF4 A 703 " - pdb=" SG CYS A 192 " pdb=" SF4 A 704 " pdb="FE1 SF4 A 704 " - pdb=" SG CYS A 264 " pdb="FE2 SF4 A 704 " - pdb=" SG CYS A 232 " pdb="FE3 SF4 A 704 " - pdb=" SG CYS A 229 " pdb="FE4 SF4 A 704 " - pdb=" SG CYS A 236 " pdb=" SF4 A 705 " pdb="FE2 SF4 A 705 " - pdb=" ND1 HIS A 98 " pdb="FE4 SF4 A 705 " - pdb=" SG CYS A 100 " pdb="FE3 SF4 A 705 " - pdb=" SG CYS A 109 " pdb="FE1 SF4 A 705 " - pdb=" SG CYS A 103 " pdb=" SF4 B 601 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 458 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 455 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 501 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 461 " pdb=" SF4 E 201 " pdb="FE3 SF4 E 201 " - pdb=" SG CYS E 149 " pdb="FE1 SF4 E 201 " - pdb=" SG CYS E 17 " pdb="FE2 SF4 E 201 " - pdb=" SG CYS E 14 " pdb="FE4 SF4 E 201 " - pdb=" SG CYS E 85 " pdb=" SF4 F 702 " pdb="FE4 SF4 F 702 " - pdb=" SG CYS F 151 " pdb="FE2 SF4 F 702 " - pdb=" SG CYS F 148 " pdb="FE3 SF4 F 702 " - pdb=" SG CYS F 154 " pdb="FE1 SF4 F 702 " - pdb=" SG CYS F 202 " pdb=" SF4 F 703 " pdb="FE1 SF4 F 703 " - pdb=" SG CYS F 195 " pdb="FE2 SF4 F 703 " - pdb=" SG CYS F 158 " pdb="FE3 SF4 F 703 " - pdb=" SG CYS F 198 " pdb="FE4 SF4 F 703 " - pdb=" SG CYS F 192 " pdb=" SF4 F 704 " pdb="FE1 SF4 F 704 " - pdb=" SG CYS F 264 " pdb="FE2 SF4 F 704 " - pdb=" SG CYS F 232 " pdb="FE3 SF4 F 704 " - pdb=" SG CYS F 229 " pdb="FE4 SF4 F 704 " - pdb=" SG CYS F 236 " pdb=" SF4 F 705 " pdb="FE2 SF4 F 705 " - pdb=" ND1 HIS F 98 " pdb="FE4 SF4 F 705 " - pdb=" SG CYS F 100 " pdb="FE3 SF4 F 705 " - pdb=" SG CYS F 109 " pdb="FE1 SF4 F 705 " - pdb=" SG CYS F 103 " pdb=" SF4 G 601 " pdb="FE1 SF4 G 601 " - pdb=" SG CYS G 458 " pdb="FE4 SF4 G 601 " - pdb=" SG CYS G 455 " pdb="FE2 SF4 G 601 " - pdb=" SG CYS G 501 " pdb="FE3 SF4 G 601 " - pdb=" SG CYS G 461 " pdb=" SF4 J 201 " pdb="FE3 SF4 J 201 " - pdb=" SG CYS J 149 " pdb="FE1 SF4 J 201 " - pdb=" SG CYS J 17 " pdb="FE2 SF4 J 201 " - pdb=" SG CYS J 14 " pdb="FE4 SF4 J 201 " - pdb=" SG CYS J 85 " Number of angles added : 170 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 26 sheets defined 37.4% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.657A 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 153 through 159 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 265 through 268 No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.686A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 276' Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.815A pdb=" N GLU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 350 through 359 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.669A pdb=" N ARG A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 removed outlier: 3.661A pdb=" N ALA A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 519 through 531 removed outlier: 3.709A pdb=" N THR A 523 " --> pdb=" O HIS A 519 " (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 609 No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 243 through 257 removed outlier: 4.283A pdb=" N MET B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) 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 308 through 311 No H-bonds generated for 'chain 'B' and resid 308 through 311' 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 327 Processing helix chain 'B' and resid 329 through 333 removed outlier: 4.034A pdb=" N ILE B 333 " --> pdb=" O PRO B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 375 through 378 No H-bonds generated for 'chain 'B' and resid 375 through 378' Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.689A pdb=" N THR B 419 " --> pdb=" O TYR B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 419' Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 459 through 476 removed outlier: 4.043A pdb=" N THR B 465 " --> pdb=" O CYS B 461 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 507 through 516 Proline residue: B 510 - end of helix removed outlier: 5.665A pdb=" N THR B 513 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'C' and resid 6 through 15 removed outlier: 3.631A pdb=" N VAL C 9 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 10 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYS C 11 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL C 12 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 14 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 15 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 19 No H-bonds generated for 'chain 'C' and resid 17 through 19' Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.831A pdb=" N VAL C 33 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 56 through 65 Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 92 through 103 Processing helix chain 'C' and resid 149 through 152 No H-bonds generated for 'chain 'C' and resid 149 through 152' Processing helix chain 'D' and resid 53 through 63 Proline residue: D 57 - end of helix removed outlier: 5.216A 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 121 Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 140 through 161 removed outlier: 3.828A pdb=" N LYS D 144 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 211 removed outlier: 3.890A pdb=" N GLN D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 3.854A 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 293 through 299 Processing helix chain 'D' and resid 306 through 318 removed outlier: 3.991A pdb=" N LYS D 310 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 348 removed outlier: 4.354A pdb=" N ALA D 333 " --> pdb=" O TYR D 330 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 346 " --> pdb=" O GLU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 417 removed outlier: 3.784A pdb=" N ASN D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA D 408 " --> pdb=" O HIS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 441 removed outlier: 4.358A pdb=" N ILE D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 3.943A 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 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 64 through 74 removed outlier: 3.566A pdb=" N ALA E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 87 No H-bonds generated for 'chain 'E' and resid 84 through 87' Processing helix chain 'E' and resid 92 through 97 removed outlier: 4.056A pdb=" N PHE E 97 " --> pdb=" O MET E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 106 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'F' and resid 21 through 28 removed outlier: 3.657A 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 153 through 159 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 265 through 268 No H-bonds generated for 'chain 'F' and resid 265 through 268' Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.686A pdb=" N THR F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU F 276 " --> pdb=" O PRO F 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 271 through 276' Processing helix chain 'F' and resid 296 through 308 removed outlier: 3.815A pdb=" N GLU F 306 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE F 307 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 336 Processing helix chain 'F' and resid 350 through 359 Processing helix chain 'F' and resid 361 through 366 Processing helix chain 'F' and resid 374 through 377 Processing helix chain 'F' and resid 395 through 407 Processing helix chain 'F' and resid 438 through 450 Processing helix chain 'F' and resid 480 through 486 removed outlier: 3.669A pdb=" N ARG F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 502 removed outlier: 3.661A pdb=" N ALA F 498 " --> pdb=" O ALA F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 516 No H-bonds generated for 'chain 'F' and resid 514 through 516' Processing helix chain 'F' and resid 519 through 531 removed outlier: 3.709A pdb=" N THR F 523 " --> pdb=" O HIS F 519 " (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 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 131 through 137 Processing helix chain 'G' and resid 141 through 148 Processing helix chain 'G' and resid 152 through 161 Processing helix chain 'G' and resid 174 through 182 Processing helix chain 'G' and resid 204 through 211 Processing helix chain 'G' and resid 215 through 227 Processing helix chain 'G' and resid 243 through 257 removed outlier: 4.283A pdb=" N MET G 257 " --> pdb=" O GLN G 253 " (cutoff:3.500A) 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 308 through 311 No H-bonds generated for 'chain 'G' and resid 308 through 311' 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 327 Processing helix chain 'G' and resid 329 through 333 removed outlier: 4.034A pdb=" N ILE G 333 " --> pdb=" O PRO G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 341 Processing helix chain 'G' and resid 375 through 378 No H-bonds generated for 'chain 'G' and resid 375 through 378' Processing helix chain 'G' and resid 386 through 388 No H-bonds generated for 'chain 'G' and resid 386 through 388' Processing helix chain 'G' and resid 415 through 419 removed outlier: 3.689A pdb=" N THR G 419 " --> pdb=" O TYR G 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 415 through 419' Processing helix chain 'G' and resid 439 through 452 Processing helix chain 'G' and resid 459 through 476 removed outlier: 4.043A pdb=" N THR G 465 " --> pdb=" O CYS G 461 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS G 466 " --> pdb=" O ARG G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 498 Processing helix chain 'G' and resid 507 through 516 Proline residue: G 510 - end of helix removed outlier: 5.665A pdb=" N THR G 513 " --> pdb=" O PRO G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 525 Processing helix chain 'H' and resid 6 through 15 removed outlier: 3.631A pdb=" N VAL H 9 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU H 10 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYS H 11 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL H 12 " --> pdb=" O VAL H 9 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU H 14 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE H 15 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 19 No H-bonds generated for 'chain 'H' and resid 17 through 19' Processing helix chain 'H' and resid 27 through 37 removed outlier: 3.831A pdb=" N VAL H 33 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 52 Processing helix chain 'H' and resid 56 through 65 Processing helix chain 'H' and resid 85 through 90 Processing helix chain 'H' and resid 92 through 103 Processing helix chain 'H' and resid 149 through 152 No H-bonds generated for 'chain 'H' and resid 149 through 152' Processing helix chain 'I' and resid 53 through 63 Proline residue: I 57 - end of helix removed outlier: 5.216A 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 121 Processing helix chain 'I' and resid 132 through 138 Processing helix chain 'I' and resid 140 through 161 removed outlier: 3.828A pdb=" N LYS I 144 " --> pdb=" O PRO I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 211 removed outlier: 3.890A pdb=" N GLN I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) removed outlier: 3.854A 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 293 through 299 Processing helix chain 'I' and resid 306 through 318 removed outlier: 3.991A pdb=" N LYS I 310 " --> pdb=" O PRO I 306 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU I 311 " --> pdb=" O GLU I 307 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET I 318 " --> pdb=" O LEU I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 328 through 348 removed outlier: 4.354A pdb=" N ALA I 333 " --> pdb=" O TYR I 330 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU I 346 " --> pdb=" O GLU I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 401 through 417 removed outlier: 3.784A pdb=" N ASN I 405 " --> pdb=" O ALA I 401 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE I 407 " --> pdb=" O GLY I 403 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA I 408 " --> pdb=" O HIS I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 441 removed outlier: 4.358A pdb=" N ILE I 438 " --> pdb=" O LEU I 434 " (cutoff:3.500A) removed outlier: 3.943A 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 19 No H-bonds generated for 'chain 'J' and resid 16 through 19' Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 64 through 74 removed outlier: 3.566A pdb=" N ALA J 69 " --> pdb=" O GLU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 87 No H-bonds generated for 'chain 'J' and resid 84 through 87' Processing helix chain 'J' and resid 92 through 97 removed outlier: 4.056A pdb=" N PHE J 97 " --> pdb=" O MET J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 106 Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 173 through 175 No H-bonds generated for 'chain 'J' and resid 173 through 175' 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 51 through 53 Processing sheet with id= C, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= D, first strand: chain 'A' and resid 223 through 228 Processing sheet with id= E, first strand: chain 'A' and resid 316 through 319 removed outlier: 6.586A pdb=" N PHE A 572 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE A 319 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR A 574 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 508 through 511 removed outlier: 6.094A pdb=" N LYS A 411 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR A 385 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET A 413 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASN A 414 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP A 429 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 8.046A pdb=" N LYS B 189 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY B 232 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL B 191 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE B 234 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS B 193 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N CYS B 236 " --> pdb=" O CYS B 193 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 391 through 395 removed outlier: 6.990A pdb=" N MET B 433 " --> pdb=" O LYS B 392 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL B 394 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 431 " --> pdb=" O VAL B 394 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 5 through 8 removed outlier: 4.250A pdb=" N PHE D 5 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 226 through 230 Processing sheet with id= K, first strand: chain 'D' and resid 264 through 267 Processing sheet with id= L, first strand: chain 'D' and resid 369 through 376 Processing sheet with id= M, first strand: chain 'E' and resid 53 through 57 removed outlier: 6.460A pdb=" N TYR E 78 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU E 56 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL E 80 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL E 144 " --> pdb=" O ALA E 81 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= O, first strand: chain 'F' and resid 51 through 53 Processing sheet with id= P, first strand: chain 'F' and resid 141 through 143 Processing sheet with id= Q, first strand: chain 'F' and resid 223 through 228 Processing sheet with id= R, first strand: chain 'F' and resid 316 through 319 removed outlier: 6.586A pdb=" N PHE F 572 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE F 319 " --> pdb=" O PHE F 572 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR F 574 " --> pdb=" O ILE F 319 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 508 through 511 removed outlier: 6.094A pdb=" N LYS F 411 " --> pdb=" O ILE F 383 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR F 385 " --> pdb=" O LYS F 411 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET F 413 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASN F 414 " --> pdb=" O ASP F 427 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP F 429 " --> pdb=" O ASN F 414 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 276 through 278 removed outlier: 8.046A pdb=" N LYS G 189 " --> pdb=" O ASP G 230 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY G 232 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL G 191 " --> pdb=" O GLY G 232 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE G 234 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS G 193 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N CYS G 236 " --> pdb=" O CYS G 193 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 391 through 395 removed outlier: 6.990A pdb=" N MET G 433 " --> pdb=" O LYS G 392 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL G 394 " --> pdb=" O VAL G 431 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL G 431 " --> pdb=" O VAL G 394 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 5 through 8 removed outlier: 4.250A pdb=" N PHE I 5 " --> pdb=" O LEU I 25 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 226 through 230 Processing sheet with id= X, first strand: chain 'I' and resid 264 through 267 Processing sheet with id= Y, first strand: chain 'I' and resid 369 through 376 Processing sheet with id= Z, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.460A pdb=" N TYR J 78 " --> pdb=" O GLY J 54 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU J 56 " --> pdb=" O TYR J 78 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL J 80 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL J 144 " --> pdb=" O ALA J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z 830 hydrogen bonds defined for protein. 2286 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: 8.83 Time building geometry restraints manager: 12.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.37: 10042 1.37 - 1.60: 19308 1.60 - 1.82: 338 1.82 - 2.05: 0 2.05 - 2.27: 168 Bond restraints: 29856 Sorted by residual: bond pdb=" C1 FCO D 602 " pdb="FE FCO D 602 " ideal model delta sigma weight residual 1.940 1.791 0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" C1 FCO I 602 " pdb="FE FCO I 602 " ideal model delta sigma weight residual 1.940 1.791 0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" CA SER A 227 " pdb=" CB SER A 227 " ideal model delta sigma weight residual 1.542 1.477 0.066 8.90e-03 1.26e+04 5.46e+01 bond pdb=" CA SER F 227 " pdb=" CB SER F 227 " ideal model delta sigma weight residual 1.542 1.477 0.066 8.90e-03 1.26e+04 5.46e+01 bond pdb=" C2 FCO D 602 " pdb="FE FCO D 602 " ideal model delta sigma weight residual 1.939 1.793 0.146 2.00e-02 2.50e+03 5.35e+01 ... (remaining 29851 not shown) Histogram of bond angle deviations from ideal: 71.47 - 92.35: 172 92.35 - 113.23: 16323 113.23 - 134.12: 23955 134.12 - 155.00: 4 155.00 - 175.88: 6 Bond angle restraints: 40460 Sorted by residual: angle pdb=" C1 FCO I 602 " pdb="FE FCO I 602 " pdb=" C3 FCO I 602 " ideal model delta sigma weight residual 180.00 92.69 87.31 3.00e+00 1.11e-01 8.47e+02 angle pdb=" C1 FCO D 602 " pdb="FE FCO D 602 " pdb=" C3 FCO D 602 " ideal model delta sigma weight residual 180.00 92.69 87.31 3.00e+00 1.11e-01 8.47e+02 angle pdb=" S1 FES H 501 " pdb="FE2 FES H 501 " pdb=" S2 FES H 501 " ideal model delta sigma weight residual 104.33 86.63 17.70 1.14e+00 7.69e-01 2.41e+02 angle pdb=" S1 FES C 501 " pdb="FE2 FES C 501 " pdb=" S2 FES C 501 " ideal model delta sigma weight residual 104.33 86.63 17.70 1.14e+00 7.69e-01 2.41e+02 angle pdb=" S1 FES C 501 " pdb="FE1 FES C 501 " pdb=" S2 FES C 501 " ideal model delta sigma weight residual 104.33 86.64 17.69 1.20e+00 6.94e-01 2.17e+02 ... (remaining 40455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15825 17.91 - 35.82: 1757 35.82 - 53.73: 376 53.73 - 71.64: 70 71.64 - 89.55: 38 Dihedral angle restraints: 18066 sinusoidal: 7376 harmonic: 10690 Sorted by residual: dihedral pdb=" N PRO F 230 " pdb=" C PRO F 230 " pdb=" CA PRO F 230 " pdb=" CB PRO F 230 " ideal model delta harmonic sigma weight residual 115.10 99.56 15.54 0 2.50e+00 1.60e-01 3.86e+01 dihedral pdb=" CA SER E 113 " pdb=" C SER E 113 " pdb=" N THR E 114 " pdb=" CA THR E 114 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA SER J 113 " pdb=" C SER J 113 " pdb=" N THR J 114 " pdb=" CA THR J 114 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 18063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.300: 4490 0.300 - 0.601: 4 0.601 - 0.901: 8 0.901 - 1.202: 22 1.202 - 1.502: 8 Chirality restraints: 4532 Sorted by residual: chirality pdb="FE1 SF4 A 702 " pdb=" S2 SF4 A 702 " pdb=" S3 SF4 A 702 " pdb=" S4 SF4 A 702 " both_signs ideal model delta sigma weight residual False -10.55 -9.05 -1.50 2.00e-01 2.50e+01 5.64e+01 chirality pdb="FE1 SF4 F 702 " pdb=" S2 SF4 F 702 " pdb=" S3 SF4 F 702 " pdb=" S4 SF4 F 702 " both_signs ideal model delta sigma weight residual False -10.55 -9.05 -1.50 2.00e-01 2.50e+01 5.64e+01 chirality pdb="FE3 SF4 A 702 " pdb=" S1 SF4 A 702 " pdb=" S2 SF4 A 702 " pdb=" S4 SF4 A 702 " both_signs ideal model delta sigma weight residual False -10.55 -9.28 -1.28 2.00e-01 2.50e+01 4.08e+01 ... (remaining 4529 not shown) Planarity restraints: 5202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 190 " 0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C ASP F 190 " -0.091 2.00e-02 2.50e+03 pdb=" O ASP F 190 " 0.034 2.00e-02 2.50e+03 pdb=" N THR F 191 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 190 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C ASP A 190 " 0.091 2.00e-02 2.50e+03 pdb=" O ASP A 190 " -0.034 2.00e-02 2.50e+03 pdb=" N THR A 191 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 621 " 0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C TRP A 621 " -0.072 2.00e-02 2.50e+03 pdb=" O TRP A 621 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR A 622 " 0.024 2.00e-02 2.50e+03 ... (remaining 5199 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 162 2.51 - 3.11: 20859 3.11 - 3.71: 47813 3.71 - 4.30: 70021 4.30 - 4.90: 113029 Nonbonded interactions: 251884 Sorted by model distance: nonbonded pdb=" SG CYS I 447 " pdb="NI 3NI I 601 " model vdw 1.915 3.280 nonbonded pdb=" SG CYS D 447 " pdb="NI 3NI D 601 " model vdw 1.915 3.280 nonbonded pdb=" NH2 ARG A 606 " pdb=" OD1 ASP I 253 " model vdw 2.146 2.520 nonbonded pdb=" OD1 ASP D 253 " pdb=" NH2 ARG F 606 " model vdw 2.146 2.520 nonbonded pdb=" O THR J 111 " pdb=" OG1 THR J 111 " model vdw 2.159 2.440 ... (remaining 251879 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: 2.030 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: 0.020 Extract box with map and model: 5.350 Check model and map are aligned: 0.440 Set scattering table: 0.240 Process input model: 80.470 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.250 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 : 0.010 0.149 29856 Z= 0.675 Angle : 1.517 87.314 40460 Z= 0.881 Chirality : 0.123 1.502 4532 Planarity : 0.008 0.075 5202 Dihedral : 15.936 89.546 11208 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 5.23 % Allowed : 13.75 % Favored : 81.01 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.11), residues: 3712 helix: -2.56 (0.10), residues: 1484 sheet: -3.39 (0.22), residues: 382 loop : -3.39 (0.12), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP F 621 HIS 0.014 0.003 HIS A 165 PHE 0.023 0.003 PHE E 88 TYR 0.047 0.003 TYR F 102 ARG 0.013 0.001 ARG F 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1144 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7813 (m-30) cc_final: 0.7530 (m-30) REVERT: A 14 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7381 (mmmt) REVERT: A 38 GLN cc_start: 0.7917 (tt0) cc_final: 0.7594 (tt0) REVERT: A 80 LYS cc_start: 0.8112 (tttm) cc_final: 0.7902 (tttm) REVERT: A 108 ASP cc_start: 0.7454 (m-30) cc_final: 0.7206 (m-30) REVERT: A 120 MET cc_start: 0.8094 (ttp) cc_final: 0.7796 (ttm) REVERT: A 121 ASP cc_start: 0.6571 (m-30) cc_final: 0.6147 (m-30) REVERT: A 122 SER cc_start: 0.8077 (p) cc_final: 0.7860 (m) REVERT: A 142 MET cc_start: 0.7521 (ttt) cc_final: 0.7200 (ttp) REVERT: A 144 ASP cc_start: 0.6948 (t0) cc_final: 0.6700 (t0) REVERT: A 227 SER cc_start: 0.8544 (t) cc_final: 0.8199 (p) REVERT: A 243 ARG cc_start: 0.7761 (ttt180) cc_final: 0.7481 (ttt180) REVERT: A 251 GLU cc_start: 0.7078 (pt0) cc_final: 0.6869 (pt0) REVERT: A 273 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6676 (pp20) REVERT: A 276 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6468 (mm-30) REVERT: A 346 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6844 (m-30) REVERT: A 348 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6150 (t80) REVERT: A 354 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7586 (ttm110) REVERT: A 379 ASP cc_start: 0.8435 (p0) cc_final: 0.7235 (p0) REVERT: A 383 ILE cc_start: 0.7940 (mt) cc_final: 0.7672 (mm) REVERT: A 384 ILE cc_start: 0.7628 (mm) cc_final: 0.7397 (mm) REVERT: A 411 LYS cc_start: 0.7848 (mttt) cc_final: 0.7594 (mttt) REVERT: A 479 SER cc_start: 0.2474 (OUTLIER) cc_final: 0.1281 (p) REVERT: A 505 ARG cc_start: 0.6897 (mmt180) cc_final: 0.6663 (mmt180) REVERT: A 514 ARG cc_start: 0.7377 (tpp80) cc_final: 0.6970 (tpp80) REVERT: A 517 LYS cc_start: 0.7437 (ptmt) cc_final: 0.7082 (ptmt) REVERT: A 585 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6793 (mt-10) REVERT: A 586 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: A 632 GLU cc_start: 0.6636 (mm-30) cc_final: 0.6435 (mm-30) REVERT: A 667 GLU cc_start: 0.7425 (mp0) cc_final: 0.7171 (mp0) REVERT: A 678 PHE cc_start: 0.7615 (m-80) cc_final: 0.7147 (m-10) REVERT: B 145 LYS cc_start: 0.7713 (tppt) cc_final: 0.7475 (tppt) REVERT: B 158 GLU cc_start: 0.7514 (tp30) cc_final: 0.7118 (tp30) REVERT: B 160 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8412 (ttmt) REVERT: B 176 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7691 (tt) REVERT: B 179 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7128 (tm-30) REVERT: B 189 LYS cc_start: 0.8449 (mttp) cc_final: 0.8226 (mttm) REVERT: B 193 CYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7096 (m) REVERT: B 199 ASP cc_start: 0.7742 (t0) cc_final: 0.7428 (t0) REVERT: B 220 MET cc_start: 0.6181 (mtp) cc_final: 0.5334 (mtp) REVERT: B 274 HIS cc_start: 0.8463 (m-70) cc_final: 0.8187 (m-70) REVERT: B 277 GLU cc_start: 0.7263 (pm20) cc_final: 0.6987 (pm20) REVERT: B 295 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6897 (mt-10) REVERT: B 302 ARG cc_start: 0.7278 (mmt180) cc_final: 0.6929 (mmt180) REVERT: B 324 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7291 (tm-30) REVERT: B 339 TRP cc_start: 0.7648 (t60) cc_final: 0.7277 (t60) REVERT: B 352 LYS cc_start: 0.7638 (tptt) cc_final: 0.7102 (tptt) REVERT: B 353 ILE cc_start: 0.7943 (pt) cc_final: 0.7739 (pt) REVERT: B 361 THR cc_start: 0.6591 (OUTLIER) cc_final: 0.5887 (m) REVERT: B 396 ILE cc_start: 0.8289 (tp) cc_final: 0.8045 (tp) REVERT: B 452 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7242 (ttm110) REVERT: B 453 GLU cc_start: 0.6959 (mp0) cc_final: 0.6205 (mp0) REVERT: B 457 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7530 (ttmt) REVERT: B 474 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7380 (ttpp) REVERT: B 490 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7107 (mm-30) REVERT: B 494 MET cc_start: 0.7785 (tmm) cc_final: 0.7553 (tmm) REVERT: B 516 ARG cc_start: 0.7398 (ptm160) cc_final: 0.7172 (ptm160) REVERT: C 26 LEU cc_start: 0.8543 (tp) cc_final: 0.8107 (tt) REVERT: C 29 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8570 (tt) REVERT: C 100 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7682 (mmmm) REVERT: C 108 ASN cc_start: 0.7374 (t0) cc_final: 0.6958 (t0) REVERT: C 118 LEU cc_start: 0.7944 (tp) cc_final: 0.7697 (tp) REVERT: C 119 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7060 (mm-30) REVERT: D 13 THR cc_start: 0.8624 (p) cc_final: 0.8320 (p) REVERT: D 80 ASP cc_start: 0.7051 (m-30) cc_final: 0.6679 (m-30) REVERT: D 81 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6499 (tm-30) REVERT: D 93 LYS cc_start: 0.8232 (mttp) cc_final: 0.8004 (mttt) REVERT: D 128 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7732 (mmmt) REVERT: D 151 LYS cc_start: 0.7631 (tttm) cc_final: 0.7316 (mtpp) REVERT: D 158 LYS cc_start: 0.8395 (tttt) cc_final: 0.8153 (tttm) REVERT: D 194 MET cc_start: 0.7040 (mmt) cc_final: 0.6752 (mmt) REVERT: D 215 GLU cc_start: 0.7356 (tp30) cc_final: 0.7067 (tp30) REVERT: D 239 ASP cc_start: 0.7019 (t0) cc_final: 0.6773 (t0) REVERT: D 245 LYS cc_start: 0.8328 (mttt) cc_final: 0.8112 (mttp) REVERT: D 250 ARG cc_start: 0.8249 (mtm110) cc_final: 0.8043 (mtm-85) REVERT: D 251 ILE cc_start: 0.8727 (mp) cc_final: 0.8278 (mt) REVERT: D 253 ASP cc_start: 0.6591 (t0) cc_final: 0.6330 (t0) REVERT: D 258 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7767 (ttmt) REVERT: D 280 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7826 (ttmt) REVERT: D 389 GLU cc_start: 0.7234 (tp30) cc_final: 0.6966 (tp30) REVERT: D 397 ASN cc_start: 0.8087 (t0) cc_final: 0.7871 (t0) REVERT: D 448 SER cc_start: 0.7996 (p) cc_final: 0.7776 (p) REVERT: E 35 VAL cc_start: 0.8484 (p) cc_final: 0.8246 (m) REVERT: E 72 MET cc_start: 0.7862 (tpp) cc_final: 0.7597 (tpp) REVERT: E 75 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7789 (mtt90) REVERT: E 84 ASP cc_start: 0.7530 (m-30) cc_final: 0.7199 (m-30) REVERT: E 103 VAL cc_start: 0.8396 (t) cc_final: 0.8164 (p) REVERT: E 137 ASP cc_start: 0.6902 (p0) cc_final: 0.6683 (p0) REVERT: F 3 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6348 (mm-30) REVERT: F 7 THR cc_start: 0.8138 (m) cc_final: 0.7931 (t) REVERT: F 9 ASP cc_start: 0.7845 (m-30) cc_final: 0.7633 (m-30) REVERT: F 14 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7405 (mmmt) REVERT: F 17 GLN cc_start: 0.8174 (tp-100) cc_final: 0.7900 (tm-30) REVERT: F 38 GLN cc_start: 0.8019 (tt0) cc_final: 0.7653 (tt0) REVERT: F 77 LYS cc_start: 0.7776 (mtmm) cc_final: 0.7456 (mtmm) REVERT: F 82 LYS cc_start: 0.7950 (tttp) cc_final: 0.7741 (tttp) REVERT: F 105 GLN cc_start: 0.7450 (mm110) cc_final: 0.7116 (mm-40) REVERT: F 108 ASP cc_start: 0.7285 (m-30) cc_final: 0.6977 (m-30) REVERT: F 120 MET cc_start: 0.7970 (ttp) cc_final: 0.7655 (ttm) REVERT: F 121 ASP cc_start: 0.6575 (m-30) cc_final: 0.6166 (m-30) REVERT: F 142 MET cc_start: 0.7436 (ttt) cc_final: 0.7102 (ttp) REVERT: F 144 ASP cc_start: 0.6997 (t0) cc_final: 0.6794 (t0) REVERT: F 156 ARG cc_start: 0.7414 (mtt180) cc_final: 0.7019 (mtt90) REVERT: F 172 ARG cc_start: 0.7542 (ptm160) cc_final: 0.7300 (ttp-110) REVERT: F 175 GLN cc_start: 0.7644 (mp10) cc_final: 0.7419 (mp10) REVERT: F 177 LYS cc_start: 0.8419 (ttpp) cc_final: 0.8049 (ttmm) REVERT: F 227 SER cc_start: 0.8496 (t) cc_final: 0.8152 (p) REVERT: F 251 GLU cc_start: 0.7152 (pt0) cc_final: 0.6897 (pt0) REVERT: F 273 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6565 (pp20) REVERT: F 276 GLU cc_start: 0.6683 (mm-30) cc_final: 0.6391 (mm-30) REVERT: F 326 ASP cc_start: 0.7140 (p0) cc_final: 0.6430 (p0) REVERT: F 327 GLU cc_start: 0.7328 (mp0) cc_final: 0.6642 (mp0) REVERT: F 346 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6988 (t70) REVERT: F 348 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6147 (t80) REVERT: F 354 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7775 (ptp90) REVERT: F 379 ASP cc_start: 0.8308 (p0) cc_final: 0.7469 (p0) REVERT: F 383 ILE cc_start: 0.7953 (mt) cc_final: 0.7672 (mm) REVERT: F 411 LYS cc_start: 0.7807 (mttt) cc_final: 0.7557 (mttt) REVERT: F 479 SER cc_start: 0.2573 (OUTLIER) cc_final: 0.1075 (p) REVERT: F 514 ARG cc_start: 0.7285 (tpp80) cc_final: 0.6859 (tpp80) REVERT: F 558 VAL cc_start: 0.7669 (t) cc_final: 0.7454 (m) REVERT: F 585 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6798 (mt-10) REVERT: F 586 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: F 600 GLN cc_start: 0.7699 (tt0) cc_final: 0.7455 (tt0) REVERT: F 640 THR cc_start: 0.8206 (t) cc_final: 0.7872 (p) REVERT: F 667 GLU cc_start: 0.7294 (mp0) cc_final: 0.7041 (mp0) REVERT: F 678 PHE cc_start: 0.7592 (m-80) cc_final: 0.6998 (m-10) REVERT: G 176 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7516 (tt) REVERT: G 179 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7153 (tm-30) REVERT: G 189 LYS cc_start: 0.8427 (mttp) cc_final: 0.8196 (mttm) REVERT: G 193 CYS cc_start: 0.7603 (OUTLIER) cc_final: 0.6883 (m) REVERT: G 199 ASP cc_start: 0.7871 (t0) cc_final: 0.7565 (t0) REVERT: G 220 MET cc_start: 0.6330 (mtp) cc_final: 0.5796 (mtp) REVERT: G 274 HIS cc_start: 0.8331 (m-70) cc_final: 0.8068 (m-70) REVERT: G 276 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7994 (mmtt) REVERT: G 300 MET cc_start: 0.6598 (mmm) cc_final: 0.5904 (mmm) REVERT: G 302 ARG cc_start: 0.7350 (mmt180) cc_final: 0.7108 (mmt180) REVERT: G 324 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7414 (tm-30) REVERT: G 352 LYS cc_start: 0.7496 (tptt) cc_final: 0.6927 (tptt) REVERT: G 361 THR cc_start: 0.6488 (OUTLIER) cc_final: 0.5733 (m) REVERT: G 385 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8196 (mp) REVERT: G 396 ILE cc_start: 0.8287 (tp) cc_final: 0.8051 (tp) REVERT: G 453 GLU cc_start: 0.6853 (mp0) cc_final: 0.6138 (mp0) REVERT: G 494 MET cc_start: 0.7708 (tmm) cc_final: 0.7483 (tmm) REVERT: G 509 ASN cc_start: 0.7933 (m110) cc_final: 0.7654 (m110) REVERT: G 516 ARG cc_start: 0.7518 (ptm160) cc_final: 0.7266 (ptm160) REVERT: G 517 TYR cc_start: 0.7928 (m-80) cc_final: 0.6895 (m-10) REVERT: H 26 LEU cc_start: 0.8605 (tp) cc_final: 0.8177 (tt) REVERT: H 29 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8561 (tt) REVERT: H 36 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6540 (tm-30) REVERT: H 43 GLU cc_start: 0.7375 (mp0) cc_final: 0.6948 (mp0) REVERT: H 100 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7638 (mmmm) REVERT: H 108 ASN cc_start: 0.7330 (t0) cc_final: 0.6937 (t0) REVERT: H 118 LEU cc_start: 0.7788 (tp) cc_final: 0.7555 (tp) REVERT: H 119 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6901 (mm-30) REVERT: H 133 MET cc_start: 0.7836 (tmm) cc_final: 0.7581 (tmm) REVERT: I 13 THR cc_start: 0.8556 (p) cc_final: 0.8295 (p) REVERT: I 33 GLU cc_start: 0.6948 (pt0) cc_final: 0.6564 (pt0) REVERT: I 75 SER cc_start: 0.8068 (t) cc_final: 0.7811 (m) REVERT: I 93 LYS cc_start: 0.8170 (mttp) cc_final: 0.7963 (mttt) REVERT: I 120 LEU cc_start: 0.8344 (mt) cc_final: 0.8067 (mt) REVERT: I 128 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7665 (mmmt) REVERT: I 194 MET cc_start: 0.7147 (mmt) cc_final: 0.6881 (mmt) REVERT: I 215 GLU cc_start: 0.7146 (tp30) cc_final: 0.6811 (tp30) REVERT: I 217 LYS cc_start: 0.8184 (mttt) cc_final: 0.7957 (mttm) REVERT: I 239 ASP cc_start: 0.7084 (t0) cc_final: 0.6814 (t0) REVERT: I 251 ILE cc_start: 0.8650 (mp) cc_final: 0.8208 (mt) REVERT: I 253 ASP cc_start: 0.6570 (t0) cc_final: 0.6313 (t0) REVERT: I 258 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7713 (ttmt) REVERT: I 280 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7853 (ttmt) REVERT: I 389 GLU cc_start: 0.7238 (tp30) cc_final: 0.6966 (tp30) REVERT: I 414 GLU cc_start: 0.7302 (tt0) cc_final: 0.7012 (mt-10) REVERT: I 445 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7632 (mp) REVERT: I 448 SER cc_start: 0.8106 (p) cc_final: 0.7891 (p) REVERT: J 35 VAL cc_start: 0.8450 (p) cc_final: 0.8226 (m) REVERT: J 84 ASP cc_start: 0.7545 (m-30) cc_final: 0.7233 (m-30) REVERT: J 177 ARG cc_start: 0.7189 (mmt-90) cc_final: 0.6775 (mmt-90) outliers start: 164 outliers final: 62 residues processed: 1252 average time/residue: 0.4584 time to fit residues: 865.6973 Evaluate side-chains 1137 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1051 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 149 CYS Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 346 ASP Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 414 ASN Chi-restraints excluded: chain F residue 479 SER Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 526 CYS Chi-restraints excluded: chain F residue 537 GLU Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 674 CYS Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 193 CYS Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 385 ILE Chi-restraints excluded: chain G residue 389 LYS Chi-restraints excluded: chain G residue 458 CYS Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 100 LYS Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 149 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 154 optimal weight: 0.0470 chunk 95 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 149 optimal weight: 0.0020 chunk 288 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 214 optimal weight: 5.9990 chunk 334 optimal weight: 0.8980 overall best weight: 0.4886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 69 GLN A 112 GLN A 145 HIS ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 366 GLN A 375 HIS A 391 GLN A 407 HIS A 409 ASN A 652 HIS B 505 GLN B 509 ASN C 88 HIS D 166 HIS D 267 HIS D 331 HIS D 386 GLN D 397 ASN ** D 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN E 34 ASN E 62 ASN F 26 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS F 366 GLN F 391 GLN F 407 HIS F 409 ASN F 652 HIS G 505 GLN H 88 HIS H 149 GLN I 166 HIS I 267 HIS I 331 HIS I 386 GLN ** I 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 ASN J 34 ASN J 62 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29856 Z= 0.196 Angle : 0.645 10.048 40460 Z= 0.329 Chirality : 0.046 0.189 4532 Planarity : 0.006 0.073 5202 Dihedral : 7.841 67.305 4245 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.63 % Allowed : 19.18 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % 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: -3.34 (0.12), residues: 3712 helix: -1.30 (0.13), residues: 1480 sheet: -3.03 (0.25), residues: 348 loop : -2.87 (0.12), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 339 HIS 0.005 0.001 HIS A 375 PHE 0.016 0.001 PHE A 572 TYR 0.018 0.001 TYR D 139 ARG 0.008 0.000 ARG F 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1087 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7920 (m-30) cc_final: 0.7548 (m-30) REVERT: A 14 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7311 (mmmt) REVERT: A 38 GLN cc_start: 0.7795 (tt0) cc_final: 0.7522 (tt0) REVERT: A 86 ARG cc_start: 0.7808 (ttt-90) cc_final: 0.7596 (ttt-90) REVERT: A 120 MET cc_start: 0.8011 (ttp) cc_final: 0.7776 (ttp) REVERT: A 144 ASP cc_start: 0.6816 (t0) cc_final: 0.6551 (t0) REVERT: A 156 ARG cc_start: 0.7451 (mmt180) cc_final: 0.6728 (mtt90) REVERT: A 172 ARG cc_start: 0.7563 (ttp-110) cc_final: 0.7220 (ttp-110) REVERT: A 184 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7769 (mttm) REVERT: A 239 LYS cc_start: 0.7847 (tttp) cc_final: 0.7561 (tttp) REVERT: A 243 ARG cc_start: 0.7689 (ttt180) cc_final: 0.7422 (ttt180) REVERT: A 251 GLU cc_start: 0.6934 (pt0) cc_final: 0.6629 (pt0) REVERT: A 273 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6732 (pp20) REVERT: A 348 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6324 (t80) REVERT: A 379 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7189 (p0) REVERT: A 383 ILE cc_start: 0.7944 (mt) cc_final: 0.7539 (mm) REVERT: A 384 ILE cc_start: 0.7621 (mm) cc_final: 0.7406 (mm) REVERT: A 505 ARG cc_start: 0.6939 (mmt180) cc_final: 0.6730 (mmt180) REVERT: A 514 ARG cc_start: 0.7447 (tpp80) cc_final: 0.6860 (tpp80) REVERT: A 517 LYS cc_start: 0.7490 (ptmt) cc_final: 0.7209 (ptmt) REVERT: A 552 LEU cc_start: 0.7234 (tt) cc_final: 0.7031 (tt) REVERT: A 586 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: A 622 TYR cc_start: 0.7470 (p90) cc_final: 0.7038 (p90) REVERT: A 632 GLU cc_start: 0.6498 (mm-30) cc_final: 0.6291 (mm-30) REVERT: A 649 LYS cc_start: 0.3702 (OUTLIER) cc_final: 0.2984 (pttm) REVERT: B 138 ASP cc_start: 0.7234 (t0) cc_final: 0.6944 (t0) REVERT: B 160 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8238 (ttmt) REVERT: B 179 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7013 (tm-30) REVERT: B 182 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7764 (mtpt) REVERT: B 199 ASP cc_start: 0.7639 (t0) cc_final: 0.7357 (t0) REVERT: B 206 ARG cc_start: 0.7240 (ttt-90) cc_final: 0.7018 (ttt180) REVERT: B 274 HIS cc_start: 0.8462 (m-70) cc_final: 0.8204 (m-70) REVERT: B 291 MET cc_start: 0.7246 (mtm) cc_final: 0.6438 (mtm) REVERT: B 295 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6817 (mt-10) REVERT: B 302 ARG cc_start: 0.7304 (mmt180) cc_final: 0.6922 (mmt180) REVERT: B 324 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7132 (tm-30) REVERT: B 339 TRP cc_start: 0.7612 (t60) cc_final: 0.7278 (t60) REVERT: B 349 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6919 (ttpt) REVERT: B 352 LYS cc_start: 0.7683 (tptt) cc_final: 0.7214 (tptt) REVERT: B 361 THR cc_start: 0.6695 (OUTLIER) cc_final: 0.6011 (m) REVERT: B 396 ILE cc_start: 0.8263 (tp) cc_final: 0.7962 (tp) REVERT: B 452 ARG cc_start: 0.7519 (ttp-110) cc_final: 0.7313 (ttp-110) REVERT: B 453 GLU cc_start: 0.6817 (mp0) cc_final: 0.6236 (mp0) REVERT: B 466 LYS cc_start: 0.8038 (tptm) cc_final: 0.7364 (mmmm) REVERT: B 471 MET cc_start: 0.7023 (mtm) cc_final: 0.6814 (mtp) REVERT: B 487 LYS cc_start: 0.8285 (mttt) cc_final: 0.8066 (mttt) REVERT: B 494 MET cc_start: 0.7790 (tmm) cc_final: 0.7565 (tmm) REVERT: C 26 LEU cc_start: 0.8397 (tp) cc_final: 0.7988 (tt) REVERT: C 43 GLU cc_start: 0.7358 (mp0) cc_final: 0.7098 (mp0) REVERT: C 48 ILE cc_start: 0.8542 (mt) cc_final: 0.8319 (mp) REVERT: C 100 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7862 (mmmm) REVERT: C 119 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6775 (mm-30) REVERT: D 13 THR cc_start: 0.8639 (p) cc_final: 0.8346 (p) REVERT: D 52 ASP cc_start: 0.7358 (t0) cc_final: 0.7149 (t0) REVERT: D 80 ASP cc_start: 0.7015 (m-30) cc_final: 0.6640 (m-30) REVERT: D 81 GLU cc_start: 0.6687 (tm-30) cc_final: 0.6479 (tm-30) REVERT: D 93 LYS cc_start: 0.8364 (mttp) cc_final: 0.8042 (mttt) REVERT: D 118 ASP cc_start: 0.7774 (m-30) cc_final: 0.7164 (m-30) REVERT: D 128 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7631 (mmmt) REVERT: D 139 TYR cc_start: 0.7797 (m-80) cc_final: 0.7149 (m-80) REVERT: D 141 GLU cc_start: 0.7034 (pp20) cc_final: 0.6598 (pp20) REVERT: D 158 LYS cc_start: 0.8364 (tttt) cc_final: 0.8109 (tttm) REVERT: D 194 MET cc_start: 0.7075 (mmt) cc_final: 0.6816 (mmt) REVERT: D 195 LYS cc_start: 0.7726 (mttt) cc_final: 0.7480 (mtmm) REVERT: D 214 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6917 (mm-30) REVERT: D 250 ARG cc_start: 0.8187 (mtm110) cc_final: 0.7966 (mtm-85) REVERT: D 251 ILE cc_start: 0.8625 (mp) cc_final: 0.8423 (mt) REVERT: D 253 ASP cc_start: 0.6681 (t0) cc_final: 0.6437 (t0) REVERT: D 261 LEU cc_start: 0.8017 (mt) cc_final: 0.7754 (mm) REVERT: D 280 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7836 (ttmt) REVERT: D 346 GLU cc_start: 0.7207 (tt0) cc_final: 0.6996 (mt-10) REVERT: D 389 GLU cc_start: 0.7226 (tp30) cc_final: 0.6993 (tp30) REVERT: D 414 GLU cc_start: 0.7189 (tt0) cc_final: 0.6843 (mt-10) REVERT: D 418 LYS cc_start: 0.8398 (mttm) cc_final: 0.8166 (mttp) REVERT: E 35 VAL cc_start: 0.8343 (p) cc_final: 0.8134 (m) REVERT: E 72 MET cc_start: 0.7877 (tpp) cc_final: 0.7539 (tpp) REVERT: E 75 ARG cc_start: 0.7993 (mtt90) cc_final: 0.7757 (mtt90) REVERT: E 79 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8207 (tp) REVERT: E 84 ASP cc_start: 0.7455 (m-30) cc_final: 0.7051 (m-30) REVERT: F 3 GLU cc_start: 0.6748 (mm-30) cc_final: 0.5931 (mm-30) REVERT: F 9 ASP cc_start: 0.7884 (m-30) cc_final: 0.7671 (m-30) REVERT: F 14 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7365 (mmmt) REVERT: F 77 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7492 (mtmm) REVERT: F 82 LYS cc_start: 0.8008 (tttp) cc_final: 0.7769 (tttp) REVERT: F 86 ARG cc_start: 0.7705 (ttt-90) cc_final: 0.7477 (ttt-90) REVERT: F 105 GLN cc_start: 0.7304 (mm110) cc_final: 0.6900 (mm-40) REVERT: F 117 GLU cc_start: 0.7505 (tt0) cc_final: 0.6862 (tt0) REVERT: F 119 GLU cc_start: 0.7075 (mp0) cc_final: 0.6650 (mp0) REVERT: F 120 MET cc_start: 0.7879 (ttp) cc_final: 0.7670 (ttm) REVERT: F 142 MET cc_start: 0.7335 (ttt) cc_final: 0.7054 (ttp) REVERT: F 144 ASP cc_start: 0.6922 (t0) cc_final: 0.6674 (t0) REVERT: F 156 ARG cc_start: 0.7374 (mmt180) cc_final: 0.6797 (mtt90) REVERT: F 175 GLN cc_start: 0.7611 (mp10) cc_final: 0.7393 (mp10) REVERT: F 177 LYS cc_start: 0.8382 (ttpp) cc_final: 0.8077 (ttmm) REVERT: F 251 GLU cc_start: 0.7090 (pt0) cc_final: 0.6751 (pt0) REVERT: F 273 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6474 (pp20) REVERT: F 324 CYS cc_start: 0.7319 (m) cc_final: 0.7062 (m) REVERT: F 326 ASP cc_start: 0.7104 (p0) cc_final: 0.6342 (p0) REVERT: F 327 GLU cc_start: 0.7341 (mp0) cc_final: 0.6585 (mp0) REVERT: F 348 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6415 (t80) REVERT: F 369 ARG cc_start: 0.7505 (ttt180) cc_final: 0.7062 (ttt-90) REVERT: F 379 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7511 (p0) REVERT: F 383 ILE cc_start: 0.7960 (mt) cc_final: 0.7630 (mm) REVERT: F 586 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7100 (tp30) REVERT: F 604 LYS cc_start: 0.8267 (mmmm) cc_final: 0.8064 (mmtp) REVERT: F 611 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7645 (pp) REVERT: F 649 LYS cc_start: 0.4215 (OUTLIER) cc_final: 0.3675 (pttm) REVERT: G 138 ASP cc_start: 0.7450 (t0) cc_final: 0.6983 (t0) REVERT: G 179 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7011 (tm-30) REVERT: G 189 LYS cc_start: 0.8402 (mttp) cc_final: 0.8164 (mttm) REVERT: G 231 GLU cc_start: 0.6859 (tp30) cc_final: 0.6152 (tp30) REVERT: G 274 HIS cc_start: 0.8163 (m-70) cc_final: 0.7725 (m-70) REVERT: G 300 MET cc_start: 0.6424 (mmm) cc_final: 0.5868 (mmm) REVERT: G 302 ARG cc_start: 0.7342 (mmt180) cc_final: 0.7049 (mmt180) REVERT: G 324 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7295 (tm-30) REVERT: G 352 LYS cc_start: 0.7484 (tptt) cc_final: 0.6948 (tptt) REVERT: G 361 THR cc_start: 0.6557 (OUTLIER) cc_final: 0.5789 (m) REVERT: G 375 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7571 (mtt-85) REVERT: G 396 ILE cc_start: 0.8277 (tp) cc_final: 0.8002 (tp) REVERT: G 407 GLU cc_start: 0.6645 (tm-30) cc_final: 0.6274 (tm-30) REVERT: G 430 LEU cc_start: 0.7527 (pp) cc_final: 0.7241 (pt) REVERT: G 452 ARG cc_start: 0.7325 (ttp-110) cc_final: 0.6659 (ttp80) REVERT: G 453 GLU cc_start: 0.6938 (mp0) cc_final: 0.6000 (mp0) REVERT: G 494 MET cc_start: 0.7764 (tmm) cc_final: 0.7548 (tmm) REVERT: H 29 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8525 (tt) REVERT: H 30 LEU cc_start: 0.8223 (mt) cc_final: 0.7936 (mp) REVERT: H 36 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6629 (tm-30) REVERT: H 43 GLU cc_start: 0.7316 (mp0) cc_final: 0.6963 (mp0) REVERT: H 100 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7845 (mmmm) REVERT: H 119 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6636 (mm-30) REVERT: H 133 MET cc_start: 0.7585 (tmm) cc_final: 0.7234 (tmm) REVERT: I 13 THR cc_start: 0.8605 (p) cc_final: 0.8339 (p) REVERT: I 52 ASP cc_start: 0.7413 (t0) cc_final: 0.7203 (t0) REVERT: I 75 SER cc_start: 0.8039 (t) cc_final: 0.7718 (p) REVERT: I 80 ASP cc_start: 0.7026 (m-30) cc_final: 0.6659 (m-30) REVERT: I 93 LYS cc_start: 0.8272 (mttp) cc_final: 0.8044 (mttt) REVERT: I 128 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7564 (mmmt) REVERT: I 139 TYR cc_start: 0.7749 (m-80) cc_final: 0.7158 (m-80) REVERT: I 160 LEU cc_start: 0.8122 (mt) cc_final: 0.7878 (mm) REVERT: I 194 MET cc_start: 0.7187 (mmt) cc_final: 0.6970 (mmt) REVERT: I 206 LYS cc_start: 0.8251 (ttmm) cc_final: 0.7997 (ttmm) REVERT: I 217 LYS cc_start: 0.8152 (mttt) cc_final: 0.7902 (mttm) REVERT: I 253 ASP cc_start: 0.6692 (t0) cc_final: 0.6150 (t0) REVERT: I 261 LEU cc_start: 0.7994 (mt) cc_final: 0.7746 (mm) REVERT: I 280 LYS cc_start: 0.8083 (ttmt) cc_final: 0.7836 (ttmt) REVERT: I 289 TYR cc_start: 0.8237 (p90) cc_final: 0.7957 (p90) REVERT: I 346 GLU cc_start: 0.7192 (tt0) cc_final: 0.6975 (mt-10) REVERT: I 389 GLU cc_start: 0.7220 (tp30) cc_final: 0.7012 (tp30) REVERT: I 414 GLU cc_start: 0.7253 (tt0) cc_final: 0.6925 (mt-10) REVERT: I 419 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.8004 (ttpp) REVERT: I 442 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6347 (m-30) REVERT: J 38 LEU cc_start: 0.8507 (mm) cc_final: 0.8205 (mp) REVERT: J 72 MET cc_start: 0.7957 (tpp) cc_final: 0.7695 (tpp) REVERT: J 84 ASP cc_start: 0.7410 (m-30) cc_final: 0.6973 (m-30) REVERT: J 108 TYR cc_start: 0.8587 (m-80) cc_final: 0.8286 (m-80) REVERT: J 137 ASP cc_start: 0.6504 (p0) cc_final: 0.6273 (p0) outliers start: 145 outliers final: 69 residues processed: 1160 average time/residue: 0.4732 time to fit residues: 823.5290 Evaluate side-chains 1113 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1023 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 621 TRP 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 660 LYS Chi-restraints excluded: chain F residue 674 CYS Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 525 HIS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 100 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 419 LYS Chi-restraints excluded: chain I residue 421 ILE Chi-restraints excluded: chain I residue 442 ASP Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 278 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 334 optimal weight: 0.9980 chunk 361 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 397 ASN ** D 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN E 62 ASN E 116 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 97 ASN F 118 HIS F 366 GLN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS G 509 ASN I 18 HIS I 405 ASN J 34 ASN J 116 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29856 Z= 0.263 Angle : 0.653 9.025 40460 Z= 0.331 Chirality : 0.047 0.174 4532 Planarity : 0.005 0.058 5202 Dihedral : 7.045 59.916 4156 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 5.46 % Allowed : 21.03 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.13), residues: 3712 helix: -0.90 (0.13), residues: 1506 sheet: -2.88 (0.25), residues: 340 loop : -2.67 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 621 HIS 0.006 0.001 HIS A 165 PHE 0.027 0.001 PHE G 271 TYR 0.014 0.001 TYR I 279 ARG 0.006 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1055 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7897 (m-30) cc_final: 0.7554 (m-30) REVERT: A 14 LYS cc_start: 0.7745 (mmmt) cc_final: 0.7341 (mmmt) REVERT: A 86 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7599 (ttt-90) REVERT: A 120 MET cc_start: 0.8083 (ttp) cc_final: 0.7830 (ttm) REVERT: A 142 MET cc_start: 0.7435 (ttt) cc_final: 0.7128 (ttp) REVERT: A 146 ASN cc_start: 0.7577 (p0) cc_final: 0.6668 (p0) REVERT: A 156 ARG cc_start: 0.7480 (mmt180) cc_final: 0.6444 (mtt180) REVERT: A 184 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7871 (mttm) REVERT: A 232 CYS cc_start: 0.5322 (p) cc_final: 0.5040 (p) REVERT: A 239 LYS cc_start: 0.7984 (tttp) cc_final: 0.7668 (tttp) REVERT: A 273 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6778 (pp20) REVERT: A 327 GLU cc_start: 0.7334 (mp0) cc_final: 0.6579 (mp0) REVERT: A 328 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 346 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7069 (m-30) REVERT: A 348 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6335 (t80) REVERT: A 379 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.7654 (p0) REVERT: A 383 ILE cc_start: 0.7954 (mt) cc_final: 0.7645 (mm) REVERT: A 384 ILE cc_start: 0.7647 (mm) cc_final: 0.7428 (mm) REVERT: A 386 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7171 (ptm) REVERT: A 505 ARG cc_start: 0.6973 (mmt180) cc_final: 0.6755 (mmt180) REVERT: A 514 ARG cc_start: 0.7383 (tpp80) cc_final: 0.6677 (tpp80) REVERT: A 517 LYS cc_start: 0.7583 (ptmt) cc_final: 0.7286 (ptmt) REVERT: A 552 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7253 (tt) REVERT: A 611 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7720 (pp) REVERT: A 632 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6368 (tp30) REVERT: A 649 LYS cc_start: 0.3580 (OUTLIER) cc_final: 0.2856 (pttm) REVERT: A 678 PHE cc_start: 0.7600 (m-80) cc_final: 0.7126 (m-10) REVERT: B 138 ASP cc_start: 0.7206 (t0) cc_final: 0.6834 (t0) REVERT: B 145 LYS cc_start: 0.7879 (tppt) cc_final: 0.7622 (tppt) REVERT: B 149 GLU cc_start: 0.6665 (mp0) cc_final: 0.6328 (mp0) REVERT: B 160 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8270 (ttmt) REVERT: B 182 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7698 (mtpt) REVERT: B 226 VAL cc_start: 0.8612 (t) cc_final: 0.8408 (p) REVERT: B 291 MET cc_start: 0.7262 (mtm) cc_final: 0.6690 (mtm) REVERT: B 295 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7077 (mt-10) REVERT: B 302 ARG cc_start: 0.7299 (mmt180) cc_final: 0.6959 (mmt180) REVERT: B 324 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7314 (tm-30) REVERT: B 339 TRP cc_start: 0.7623 (t60) cc_final: 0.7356 (t60) REVERT: B 349 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6981 (ttpt) REVERT: B 352 LYS cc_start: 0.7557 (tptt) cc_final: 0.7107 (tptt) REVERT: B 361 THR cc_start: 0.6728 (OUTLIER) cc_final: 0.6060 (m) REVERT: B 396 ILE cc_start: 0.8283 (tp) cc_final: 0.7993 (tp) REVERT: B 466 LYS cc_start: 0.8006 (tptm) cc_final: 0.7283 (mmmm) REVERT: B 487 LYS cc_start: 0.8250 (mttt) cc_final: 0.8035 (mttt) REVERT: B 494 MET cc_start: 0.7781 (tmm) cc_final: 0.7523 (tmm) REVERT: B 517 TYR cc_start: 0.8098 (m-80) cc_final: 0.7884 (m-10) REVERT: C 36 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6858 (tm-30) REVERT: C 43 GLU cc_start: 0.7393 (mp0) cc_final: 0.7138 (mp0) REVERT: C 48 ILE cc_start: 0.8618 (mt) cc_final: 0.8399 (mp) REVERT: C 100 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7892 (mmmm) REVERT: C 119 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6774 (mm-30) REVERT: D 13 THR cc_start: 0.8628 (p) cc_final: 0.8341 (p) REVERT: D 52 ASP cc_start: 0.7343 (t0) cc_final: 0.7120 (t0) REVERT: D 80 ASP cc_start: 0.7011 (m-30) cc_final: 0.6652 (m-30) REVERT: D 93 LYS cc_start: 0.8396 (mttp) cc_final: 0.8084 (mttt) REVERT: D 128 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7657 (mmmt) REVERT: D 139 TYR cc_start: 0.7874 (m-80) cc_final: 0.7174 (m-80) REVERT: D 194 MET cc_start: 0.7050 (mmt) cc_final: 0.6811 (mmt) REVERT: D 250 ARG cc_start: 0.8239 (mtm110) cc_final: 0.7976 (mtm-85) REVERT: D 251 ILE cc_start: 0.8630 (mp) cc_final: 0.8392 (mt) REVERT: D 253 ASP cc_start: 0.6680 (t0) cc_final: 0.6459 (t0) REVERT: D 261 LEU cc_start: 0.8053 (mt) cc_final: 0.7843 (mm) REVERT: D 346 GLU cc_start: 0.7179 (tt0) cc_final: 0.6798 (mt-10) REVERT: D 389 GLU cc_start: 0.7242 (tp30) cc_final: 0.7022 (tp30) REVERT: D 405 ASN cc_start: 0.7849 (m-40) cc_final: 0.7552 (m-40) REVERT: D 414 GLU cc_start: 0.7209 (tt0) cc_final: 0.6847 (mt-10) REVERT: E 72 MET cc_start: 0.7913 (tpp) cc_final: 0.7511 (tpp) REVERT: E 75 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7818 (mmm-85) REVERT: E 84 ASP cc_start: 0.7537 (m-30) cc_final: 0.7086 (m-30) REVERT: F 3 GLU cc_start: 0.6659 (mm-30) cc_final: 0.5577 (mm-30) REVERT: F 14 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7434 (mmmt) REVERT: F 77 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7480 (mtmm) REVERT: F 82 LYS cc_start: 0.8042 (tttp) cc_final: 0.7771 (tttp) REVERT: F 86 ARG cc_start: 0.7636 (ttt-90) cc_final: 0.7373 (ttt-90) REVERT: F 105 GLN cc_start: 0.7477 (mm110) cc_final: 0.7020 (mm-40) REVERT: F 119 GLU cc_start: 0.7050 (mp0) cc_final: 0.6665 (mp0) REVERT: F 120 MET cc_start: 0.7926 (ttp) cc_final: 0.7693 (ttm) REVERT: F 142 MET cc_start: 0.7291 (ttt) cc_final: 0.7049 (ttp) REVERT: F 146 ASN cc_start: 0.7612 (p0) cc_final: 0.6799 (p0) REVERT: F 156 ARG cc_start: 0.7453 (mmt180) cc_final: 0.6816 (mtt90) REVERT: F 172 ARG cc_start: 0.7771 (ptm160) cc_final: 0.7234 (ttp80) REVERT: F 175 GLN cc_start: 0.7839 (mp10) cc_final: 0.7450 (mp10) REVERT: F 177 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8084 (ttmm) REVERT: F 251 GLU cc_start: 0.7111 (pt0) cc_final: 0.6826 (pt0) REVERT: F 273 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6565 (pp20) REVERT: F 324 CYS cc_start: 0.7270 (m) cc_final: 0.6938 (m) REVERT: F 327 GLU cc_start: 0.7345 (mp0) cc_final: 0.7133 (mm-30) REVERT: F 328 GLU cc_start: 0.7862 (mt-10) cc_final: 0.6917 (mt-10) REVERT: F 348 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6552 (t80) REVERT: F 379 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7560 (p0) REVERT: F 383 ILE cc_start: 0.7953 (mt) cc_final: 0.7644 (mm) REVERT: F 386 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7228 (ptp) REVERT: F 514 ARG cc_start: 0.7155 (tpp80) cc_final: 0.6884 (tpp80) REVERT: F 552 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7185 (tt) REVERT: F 577 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7696 (t) REVERT: F 586 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7123 (tp30) REVERT: F 611 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7742 (pp) REVERT: G 150 MET cc_start: 0.6497 (mmm) cc_final: 0.6074 (mmm) REVERT: G 154 GLU cc_start: 0.7421 (pt0) cc_final: 0.6973 (pt0) REVERT: G 179 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7028 (tm-30) REVERT: G 189 LYS cc_start: 0.8382 (mttp) cc_final: 0.8111 (mttm) REVERT: G 231 GLU cc_start: 0.6885 (tp30) cc_final: 0.6176 (tp30) REVERT: G 249 ILE cc_start: 0.8229 (mt) cc_final: 0.7921 (pt) REVERT: G 274 HIS cc_start: 0.8119 (m-70) cc_final: 0.7727 (m-70) REVERT: G 300 MET cc_start: 0.6493 (mmm) cc_final: 0.5952 (mmm) REVERT: G 302 ARG cc_start: 0.7332 (mmt180) cc_final: 0.7055 (mmt180) REVERT: G 323 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8027 (p) REVERT: G 324 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7010 (tm-30) REVERT: G 352 LYS cc_start: 0.7384 (tptt) cc_final: 0.6932 (tptt) REVERT: G 361 THR cc_start: 0.6530 (OUTLIER) cc_final: 0.5834 (m) REVERT: G 375 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7535 (mtt-85) REVERT: G 396 ILE cc_start: 0.8300 (tp) cc_final: 0.8035 (tp) REVERT: G 453 GLU cc_start: 0.6857 (mp0) cc_final: 0.6070 (mp0) REVERT: G 466 LYS cc_start: 0.7952 (tptm) cc_final: 0.7537 (ttmt) REVERT: G 494 MET cc_start: 0.7803 (tmm) cc_final: 0.7551 (tmm) REVERT: H 11 LYS cc_start: 0.8231 (tptp) cc_final: 0.7911 (tptp) REVERT: H 26 LEU cc_start: 0.8590 (tp) cc_final: 0.8040 (tp) REVERT: H 29 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8556 (tt) REVERT: H 30 LEU cc_start: 0.8244 (mt) cc_final: 0.7965 (mp) REVERT: H 36 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6647 (tm-30) REVERT: H 52 LEU cc_start: 0.8022 (mt) cc_final: 0.7788 (mp) REVERT: H 100 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7888 (mmmm) REVERT: H 119 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6535 (mm-30) REVERT: H 133 MET cc_start: 0.7653 (tmm) cc_final: 0.7324 (tmm) REVERT: I 13 THR cc_start: 0.8569 (p) cc_final: 0.8245 (p) REVERT: I 52 ASP cc_start: 0.7380 (t0) cc_final: 0.7179 (t0) REVERT: I 75 SER cc_start: 0.8088 (t) cc_final: 0.7751 (p) REVERT: I 80 ASP cc_start: 0.7055 (m-30) cc_final: 0.6733 (m-30) REVERT: I 128 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7554 (mmmt) REVERT: I 135 LEU cc_start: 0.7996 (tp) cc_final: 0.7786 (tp) REVERT: I 139 TYR cc_start: 0.7862 (m-80) cc_final: 0.7189 (m-80) REVERT: I 145 LYS cc_start: 0.8097 (mttt) cc_final: 0.7803 (mttp) REVERT: I 151 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7362 (tttp) REVERT: I 194 MET cc_start: 0.7215 (mmt) cc_final: 0.6996 (mmt) REVERT: I 289 TYR cc_start: 0.8188 (p90) cc_final: 0.7971 (p90) REVERT: I 332 TYR cc_start: 0.7943 (t80) cc_final: 0.7446 (t80) REVERT: I 389 GLU cc_start: 0.7272 (tp30) cc_final: 0.7051 (tp30) REVERT: I 414 GLU cc_start: 0.7273 (tt0) cc_final: 0.6992 (mt-10) REVERT: I 442 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6296 (m-30) REVERT: J 38 LEU cc_start: 0.8534 (mm) cc_final: 0.8250 (mp) REVERT: J 84 ASP cc_start: 0.7536 (m-30) cc_final: 0.7071 (m-30) REVERT: J 108 TYR cc_start: 0.8579 (m-80) cc_final: 0.8352 (m-80) REVERT: J 137 ASP cc_start: 0.6520 (p0) cc_final: 0.6303 (p0) outliers start: 171 outliers final: 92 residues processed: 1134 average time/residue: 0.4698 time to fit residues: 798.6957 Evaluate side-chains 1136 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1018 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 577 SER Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 621 TRP Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 660 LYS Chi-restraints excluded: chain F residue 674 CYS Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 193 CYS Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 525 HIS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 100 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain I residue 40 GLN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 442 ASP Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 330 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 224 optimal weight: 0.5980 chunk 335 optimal weight: 0.9990 chunk 355 optimal weight: 0.0020 chunk 175 optimal weight: 0.6980 chunk 318 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN D 397 ASN ** D 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN E 116 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS I 18 HIS ** I 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 ASN J 34 ASN ** J 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29856 Z= 0.201 Angle : 0.623 9.053 40460 Z= 0.315 Chirality : 0.045 0.187 4532 Planarity : 0.005 0.054 5202 Dihedral : 6.731 59.275 4149 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 5.74 % Allowed : 21.92 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3712 helix: -0.52 (0.13), residues: 1486 sheet: -2.72 (0.26), residues: 338 loop : -2.50 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 621 HIS 0.005 0.001 HIS A 165 PHE 0.019 0.001 PHE G 271 TYR 0.013 0.001 TYR D 289 ARG 0.006 0.000 ARG D 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1033 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.7658 (mmmt) cc_final: 0.7435 (mmmt) REVERT: A 83 ASP cc_start: 0.7323 (t0) cc_final: 0.6911 (t0) REVERT: A 86 ARG cc_start: 0.7816 (ttt-90) cc_final: 0.7613 (ttt-90) REVERT: A 120 MET cc_start: 0.8023 (ttp) cc_final: 0.7767 (ttp) REVERT: A 142 MET cc_start: 0.7435 (ttt) cc_final: 0.7146 (ttp) REVERT: A 156 ARG cc_start: 0.7447 (mmt180) cc_final: 0.6411 (mtt180) REVERT: A 175 GLN cc_start: 0.7840 (mp10) cc_final: 0.7508 (mp10) REVERT: A 184 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7888 (mttm) REVERT: A 232 CYS cc_start: 0.5323 (p) cc_final: 0.5021 (p) REVERT: A 239 LYS cc_start: 0.7959 (tttp) cc_final: 0.7602 (tttp) REVERT: A 243 ARG cc_start: 0.7675 (ttt180) cc_final: 0.7440 (ttt180) REVERT: A 273 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6628 (pp20) REVERT: A 327 GLU cc_start: 0.7342 (mp0) cc_final: 0.6550 (mp0) REVERT: A 328 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7232 (mt-10) REVERT: A 348 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6160 (t80) REVERT: A 369 ARG cc_start: 0.7619 (ttt180) cc_final: 0.7095 (ttt90) REVERT: A 379 ASP cc_start: 0.8494 (p0) cc_final: 0.7703 (p0) REVERT: A 383 ILE cc_start: 0.7946 (mt) cc_final: 0.7639 (mm) REVERT: A 384 ILE cc_start: 0.7606 (mm) cc_final: 0.7393 (mm) REVERT: A 386 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7144 (ptm) REVERT: A 505 ARG cc_start: 0.7015 (mmt180) cc_final: 0.6804 (mmt180) REVERT: A 514 ARG cc_start: 0.7236 (tpp80) cc_final: 0.6873 (tpp80) REVERT: A 583 GLU cc_start: 0.6173 (mt-10) cc_final: 0.5910 (mt-10) REVERT: A 611 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7769 (pp) REVERT: A 632 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6318 (mm-30) REVERT: A 649 LYS cc_start: 0.3362 (OUTLIER) cc_final: 0.3133 (pttm) REVERT: B 145 LYS cc_start: 0.7715 (tppt) cc_final: 0.7383 (ttmt) REVERT: B 160 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8189 (ttmt) REVERT: B 176 LEU cc_start: 0.8182 (tt) cc_final: 0.7897 (tt) REVERT: B 179 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7021 (tm-30) REVERT: B 291 MET cc_start: 0.7121 (mtm) cc_final: 0.6463 (mtm) REVERT: B 295 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6940 (mt-10) REVERT: B 302 ARG cc_start: 0.7229 (mmt180) cc_final: 0.6879 (mmt180) REVERT: B 324 GLU cc_start: 0.7540 (tm-30) cc_final: 0.6956 (tm-30) REVERT: B 349 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6529 (ttpt) REVERT: B 352 LYS cc_start: 0.7444 (tptt) cc_final: 0.6989 (tptt) REVERT: B 361 THR cc_start: 0.6698 (OUTLIER) cc_final: 0.5639 (m) REVERT: B 396 ILE cc_start: 0.8238 (tp) cc_final: 0.7944 (tp) REVERT: B 441 ASP cc_start: 0.7749 (t0) cc_final: 0.7372 (t0) REVERT: B 453 GLU cc_start: 0.6958 (mp0) cc_final: 0.6158 (mp0) REVERT: B 466 LYS cc_start: 0.7980 (tptm) cc_final: 0.7268 (mmmm) REVERT: B 487 LYS cc_start: 0.8251 (mttt) cc_final: 0.7992 (mttt) REVERT: B 494 MET cc_start: 0.7768 (tmm) cc_final: 0.7527 (tmm) REVERT: C 11 LYS cc_start: 0.8120 (tptp) cc_final: 0.7774 (tptp) REVERT: C 48 ILE cc_start: 0.8645 (mt) cc_final: 0.8395 (mp) REVERT: C 119 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6732 (mm-30) REVERT: D 13 THR cc_start: 0.8627 (p) cc_final: 0.8334 (p) REVERT: D 52 ASP cc_start: 0.7339 (t0) cc_final: 0.7100 (t0) REVERT: D 80 ASP cc_start: 0.6963 (m-30) cc_final: 0.6628 (m-30) REVERT: D 93 LYS cc_start: 0.8375 (mttp) cc_final: 0.8050 (mttt) REVERT: D 128 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7632 (mmmt) REVERT: D 139 TYR cc_start: 0.7868 (m-80) cc_final: 0.7161 (m-80) REVERT: D 141 GLU cc_start: 0.7064 (pp20) cc_final: 0.6612 (pp20) REVERT: D 151 LYS cc_start: 0.7821 (mmmt) cc_final: 0.7568 (mtpp) REVERT: D 194 MET cc_start: 0.7063 (mmt) cc_final: 0.6830 (mmt) REVERT: D 250 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7939 (mtm-85) REVERT: D 251 ILE cc_start: 0.8617 (mp) cc_final: 0.8377 (mt) REVERT: D 253 ASP cc_start: 0.6675 (t0) cc_final: 0.5998 (t0) REVERT: D 279 TYR cc_start: 0.7724 (t80) cc_final: 0.7373 (t80) REVERT: D 346 GLU cc_start: 0.7132 (tt0) cc_final: 0.6767 (mt-10) REVERT: D 389 GLU cc_start: 0.7174 (tp30) cc_final: 0.6917 (tp30) REVERT: D 414 GLU cc_start: 0.7209 (tt0) cc_final: 0.6846 (mt-10) REVERT: E 84 ASP cc_start: 0.7535 (m-30) cc_final: 0.7055 (m-30) REVERT: F 14 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7494 (mmmt) REVERT: F 83 ASP cc_start: 0.7237 (t0) cc_final: 0.6813 (t0) REVERT: F 86 ARG cc_start: 0.7741 (ttt-90) cc_final: 0.7506 (ttt-90) REVERT: F 105 GLN cc_start: 0.7523 (mm110) cc_final: 0.7063 (mm-40) REVERT: F 117 GLU cc_start: 0.7466 (tt0) cc_final: 0.6837 (tt0) REVERT: F 119 GLU cc_start: 0.7011 (mp0) cc_final: 0.6663 (mp0) REVERT: F 120 MET cc_start: 0.7857 (ttp) cc_final: 0.7646 (ttm) REVERT: F 133 GLU cc_start: 0.6846 (pp20) cc_final: 0.6367 (pp20) REVERT: F 138 ASP cc_start: 0.7928 (t0) cc_final: 0.7682 (t0) REVERT: F 142 MET cc_start: 0.7281 (ttt) cc_final: 0.7048 (ttp) REVERT: F 146 ASN cc_start: 0.7612 (p0) cc_final: 0.7140 (p0) REVERT: F 156 ARG cc_start: 0.7437 (mmt180) cc_final: 0.6447 (mtt180) REVERT: F 172 ARG cc_start: 0.7711 (ptm160) cc_final: 0.7162 (ttp80) REVERT: F 174 TRP cc_start: 0.8046 (t60) cc_final: 0.7815 (t60) REVERT: F 175 GLN cc_start: 0.7828 (mp10) cc_final: 0.7444 (mp10) REVERT: F 184 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7968 (mmtm) REVERT: F 251 GLU cc_start: 0.7089 (pt0) cc_final: 0.6818 (pt0) REVERT: F 273 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6601 (pp20) REVERT: F 324 CYS cc_start: 0.7362 (m) cc_final: 0.7084 (m) REVERT: F 327 GLU cc_start: 0.7314 (mp0) cc_final: 0.6474 (mp0) REVERT: F 348 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6507 (t80) REVERT: F 354 ARG cc_start: 0.7865 (ptp90) cc_final: 0.7632 (ptp90) REVERT: F 379 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7569 (p0) REVERT: F 383 ILE cc_start: 0.7919 (mt) cc_final: 0.7619 (mm) REVERT: F 386 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7216 (ptm) REVERT: F 517 LYS cc_start: 0.7533 (ptmt) cc_final: 0.7325 (pttt) REVERT: F 567 ARG cc_start: 0.7537 (ptp90) cc_final: 0.7161 (mtm110) REVERT: F 577 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7655 (t) REVERT: F 586 GLU cc_start: 0.7382 (tp30) cc_final: 0.7166 (tp30) REVERT: F 611 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7768 (pp) REVERT: F 640 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7998 (p) REVERT: F 649 LYS cc_start: 0.4020 (OUTLIER) cc_final: 0.3820 (pttm) REVERT: G 150 MET cc_start: 0.6449 (mmm) cc_final: 0.6084 (mmm) REVERT: G 154 GLU cc_start: 0.7393 (pt0) cc_final: 0.6907 (pt0) REVERT: G 160 LYS cc_start: 0.8268 (ttmt) cc_final: 0.8019 (ttmt) REVERT: G 179 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7000 (tm-30) REVERT: G 189 LYS cc_start: 0.8399 (mttp) cc_final: 0.8163 (mttm) REVERT: G 191 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7837 (t) REVERT: G 231 GLU cc_start: 0.6865 (tp30) cc_final: 0.6180 (tp30) REVERT: G 249 ILE cc_start: 0.8237 (mt) cc_final: 0.7924 (pt) REVERT: G 274 HIS cc_start: 0.8037 (m-70) cc_final: 0.7647 (m-70) REVERT: G 300 MET cc_start: 0.6470 (mmm) cc_final: 0.6025 (mmm) REVERT: G 302 ARG cc_start: 0.7312 (mmt180) cc_final: 0.7022 (mmt180) REVERT: G 323 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.7981 (p) REVERT: G 324 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6995 (tm-30) REVERT: G 352 LYS cc_start: 0.7219 (tptt) cc_final: 0.6835 (tptt) REVERT: G 361 THR cc_start: 0.6462 (OUTLIER) cc_final: 0.5798 (m) REVERT: G 370 MET cc_start: 0.5044 (tpp) cc_final: 0.4811 (tpp) REVERT: G 396 ILE cc_start: 0.8227 (tp) cc_final: 0.7974 (tp) REVERT: G 441 ASP cc_start: 0.7634 (t0) cc_final: 0.7209 (t0) REVERT: G 452 ARG cc_start: 0.7383 (ttp-110) cc_final: 0.6639 (ttp80) REVERT: G 453 GLU cc_start: 0.6846 (mp0) cc_final: 0.5903 (mp0) REVERT: G 466 LYS cc_start: 0.7927 (tptm) cc_final: 0.7607 (mmmm) REVERT: G 494 MET cc_start: 0.7787 (tmm) cc_final: 0.7569 (tmm) REVERT: H 11 LYS cc_start: 0.8205 (tptp) cc_final: 0.7962 (tptp) REVERT: H 29 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8547 (tt) REVERT: H 36 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6684 (tm-30) REVERT: H 43 GLU cc_start: 0.7305 (mp0) cc_final: 0.6896 (mp0) REVERT: H 119 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6544 (mm-30) REVERT: H 133 MET cc_start: 0.7594 (tmm) cc_final: 0.7274 (tmm) REVERT: I 13 THR cc_start: 0.8531 (p) cc_final: 0.8190 (p) REVERT: I 75 SER cc_start: 0.8118 (t) cc_final: 0.7751 (p) REVERT: I 80 ASP cc_start: 0.7040 (m-30) cc_final: 0.6735 (m-30) REVERT: I 118 ASP cc_start: 0.7563 (m-30) cc_final: 0.7360 (m-30) REVERT: I 128 LYS cc_start: 0.7940 (mmmt) cc_final: 0.7568 (mmmt) REVERT: I 135 LEU cc_start: 0.7932 (tp) cc_final: 0.7725 (tp) REVERT: I 139 TYR cc_start: 0.7797 (m-80) cc_final: 0.7167 (m-80) REVERT: I 145 LYS cc_start: 0.8006 (mttt) cc_final: 0.7732 (mttp) REVERT: I 151 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7296 (tttp) REVERT: I 194 MET cc_start: 0.7238 (mmt) cc_final: 0.7028 (mmt) REVERT: I 200 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6816 (tm-30) REVERT: I 258 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7957 (ttmt) REVERT: I 269 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6747 (mt-10) REVERT: I 332 TYR cc_start: 0.8012 (t80) cc_final: 0.7785 (t80) REVERT: I 346 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: I 388 ASN cc_start: 0.8299 (p0) cc_final: 0.7936 (p0) REVERT: I 389 GLU cc_start: 0.7224 (tp30) cc_final: 0.6980 (tp30) REVERT: I 414 GLU cc_start: 0.7305 (tt0) cc_final: 0.6971 (mt-10) REVERT: I 442 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6304 (m-30) REVERT: J 75 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7764 (mtm-85) REVERT: J 84 ASP cc_start: 0.7523 (m-30) cc_final: 0.7055 (m-30) REVERT: J 137 ASP cc_start: 0.6485 (p0) cc_final: 0.6238 (p0) outliers start: 180 outliers final: 104 residues processed: 1116 average time/residue: 0.4643 time to fit residues: 781.6472 Evaluate side-chains 1134 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1008 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 628 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 414 ASN Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 577 SER Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 621 TRP Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 640 THR Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 674 CYS Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 372 ILE Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 525 HIS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 346 GLU Chi-restraints excluded: chain I residue 364 LYS Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 442 ASP Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 0.0050 chunk 201 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 264 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 303 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 181 optimal weight: 0.5980 chunk 319 optimal weight: 0.3980 chunk 89 optimal weight: 10.0000 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN D 397 ASN D 405 ASN E 34 ASN E 116 ASN F 53 GLN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS I 37 HIS I 263 HIS I 405 ASN J 34 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29856 Z= 0.198 Angle : 0.623 10.052 40460 Z= 0.315 Chirality : 0.045 0.170 4532 Planarity : 0.005 0.052 5202 Dihedral : 6.448 57.252 4137 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 5.65 % Allowed : 23.10 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.27 (0.13), residues: 3712 helix: -0.27 (0.14), residues: 1458 sheet: -2.42 (0.26), residues: 358 loop : -2.38 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 339 HIS 0.005 0.001 HIS I 263 PHE 0.027 0.001 PHE B 518 TYR 0.019 0.001 TYR I 289 ARG 0.009 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1026 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.7676 (mmmt) cc_final: 0.7429 (mmmt) REVERT: A 83 ASP cc_start: 0.7327 (t0) cc_final: 0.6928 (t0) REVERT: A 86 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7599 (ttt-90) REVERT: A 120 MET cc_start: 0.8037 (ttp) cc_final: 0.7796 (ttp) REVERT: A 142 MET cc_start: 0.7434 (ttt) cc_final: 0.7142 (ttp) REVERT: A 146 ASN cc_start: 0.7563 (p0) cc_final: 0.7222 (p0) REVERT: A 156 ARG cc_start: 0.7456 (mmt180) cc_final: 0.6421 (mtt180) REVERT: A 175 GLN cc_start: 0.7851 (mp10) cc_final: 0.7522 (mp10) REVERT: A 184 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7896 (mttm) REVERT: A 232 CYS cc_start: 0.5245 (p) cc_final: 0.4933 (p) REVERT: A 239 LYS cc_start: 0.7971 (tttp) cc_final: 0.7680 (tttp) REVERT: A 243 ARG cc_start: 0.7681 (ttt180) cc_final: 0.7412 (ttt180) REVERT: A 251 GLU cc_start: 0.7014 (pt0) cc_final: 0.6759 (pt0) REVERT: A 273 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6661 (pp20) REVERT: A 327 GLU cc_start: 0.7284 (mp0) cc_final: 0.6507 (mp0) REVERT: A 328 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7240 (mt-10) REVERT: A 346 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7057 (m-30) REVERT: A 348 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6080 (t80) REVERT: A 369 ARG cc_start: 0.7626 (ttt180) cc_final: 0.7294 (ttp80) REVERT: A 379 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7687 (p0) REVERT: A 383 ILE cc_start: 0.8003 (mt) cc_final: 0.7661 (mm) REVERT: A 514 ARG cc_start: 0.7192 (tpp80) cc_final: 0.6835 (tpp80) REVERT: A 583 GLU cc_start: 0.6195 (mt-10) cc_final: 0.5916 (mt-10) REVERT: A 604 LYS cc_start: 0.8410 (mmmm) cc_final: 0.8140 (mmtp) REVERT: A 611 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7876 (pp) REVERT: A 613 ASP cc_start: 0.7399 (m-30) cc_final: 0.7112 (m-30) REVERT: A 649 LYS cc_start: 0.3227 (OUTLIER) cc_final: 0.2941 (pttm) REVERT: B 154 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7073 (pt0) REVERT: B 160 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8197 (ttmt) REVERT: B 176 LEU cc_start: 0.8170 (tt) cc_final: 0.7905 (tt) REVERT: B 179 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6999 (tm-30) REVERT: B 291 MET cc_start: 0.7064 (mtm) cc_final: 0.6437 (mtm) REVERT: B 295 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7045 (mt-10) REVERT: B 302 ARG cc_start: 0.7221 (mmt180) cc_final: 0.6792 (mmt180) REVERT: B 324 GLU cc_start: 0.7578 (tm-30) cc_final: 0.6997 (tm-30) REVERT: B 349 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6830 (ttpt) REVERT: B 352 LYS cc_start: 0.7409 (tptt) cc_final: 0.7018 (tptt) REVERT: B 396 ILE cc_start: 0.8074 (tp) cc_final: 0.7797 (tp) REVERT: B 453 GLU cc_start: 0.6902 (mp0) cc_final: 0.6265 (mp0) REVERT: B 457 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7338 (ttmt) REVERT: B 466 LYS cc_start: 0.7952 (tptm) cc_final: 0.7692 (ttmm) REVERT: B 494 MET cc_start: 0.7785 (tmm) cc_final: 0.7542 (tmm) REVERT: B 517 TYR cc_start: 0.7682 (m-10) cc_final: 0.7350 (m-10) REVERT: C 11 LYS cc_start: 0.8069 (tptp) cc_final: 0.7788 (tptp) REVERT: C 119 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6752 (mm-30) REVERT: D 23 VAL cc_start: 0.8449 (t) cc_final: 0.8147 (m) REVERT: D 52 ASP cc_start: 0.7407 (t0) cc_final: 0.7174 (t0) REVERT: D 80 ASP cc_start: 0.6982 (m-30) cc_final: 0.6626 (m-30) REVERT: D 93 LYS cc_start: 0.8364 (mttp) cc_final: 0.8039 (mttt) REVERT: D 114 LEU cc_start: 0.7615 (mt) cc_final: 0.7323 (mt) REVERT: D 118 ASP cc_start: 0.7683 (m-30) cc_final: 0.7423 (m-30) REVERT: D 128 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7629 (mmmt) REVERT: D 139 TYR cc_start: 0.7845 (m-80) cc_final: 0.7161 (m-80) REVERT: D 141 GLU cc_start: 0.7072 (pp20) cc_final: 0.6602 (pp20) REVERT: D 151 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7570 (mtpp) REVERT: D 194 MET cc_start: 0.7092 (mmt) cc_final: 0.6874 (mmt) REVERT: D 251 ILE cc_start: 0.8600 (mp) cc_final: 0.8365 (mt) REVERT: D 253 ASP cc_start: 0.6662 (t0) cc_final: 0.6201 (t0) REVERT: D 346 GLU cc_start: 0.7154 (tt0) cc_final: 0.6836 (mt-10) REVERT: D 389 GLU cc_start: 0.7152 (tp30) cc_final: 0.6876 (tp30) REVERT: D 405 ASN cc_start: 0.7881 (m-40) cc_final: 0.7506 (m-40) REVERT: D 414 GLU cc_start: 0.7227 (tt0) cc_final: 0.6846 (mt-10) REVERT: E 84 ASP cc_start: 0.7552 (m-30) cc_final: 0.7066 (m-30) REVERT: F 7 THR cc_start: 0.8157 (m) cc_final: 0.7857 (t) REVERT: F 14 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7411 (mmmt) REVERT: F 80 LYS cc_start: 0.8142 (tttm) cc_final: 0.7836 (tttt) REVERT: F 83 ASP cc_start: 0.7242 (t0) cc_final: 0.6837 (t0) REVERT: F 86 ARG cc_start: 0.7737 (ttt-90) cc_final: 0.7513 (ttt-90) REVERT: F 105 GLN cc_start: 0.7533 (mm110) cc_final: 0.7086 (mm-40) REVERT: F 117 GLU cc_start: 0.7425 (tt0) cc_final: 0.6821 (tt0) REVERT: F 119 GLU cc_start: 0.7068 (mp0) cc_final: 0.6667 (mp0) REVERT: F 120 MET cc_start: 0.7880 (ttp) cc_final: 0.7668 (ttp) REVERT: F 133 GLU cc_start: 0.6871 (pp20) cc_final: 0.6414 (pp20) REVERT: F 138 ASP cc_start: 0.7915 (t0) cc_final: 0.7657 (t0) REVERT: F 142 MET cc_start: 0.7319 (ttt) cc_final: 0.7049 (ttp) REVERT: F 146 ASN cc_start: 0.7573 (p0) cc_final: 0.6975 (p0) REVERT: F 156 ARG cc_start: 0.7444 (mmt180) cc_final: 0.6464 (mtt180) REVERT: F 172 ARG cc_start: 0.7703 (ptm160) cc_final: 0.7294 (ttp-110) REVERT: F 174 TRP cc_start: 0.8024 (t60) cc_final: 0.7808 (t60) REVERT: F 175 GLN cc_start: 0.7860 (mp10) cc_final: 0.7454 (mp10) REVERT: F 184 LYS cc_start: 0.8209 (mmtt) cc_final: 0.8005 (mmtm) REVERT: F 232 CYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5733 (p) REVERT: F 251 GLU cc_start: 0.7073 (pt0) cc_final: 0.6804 (pt0) REVERT: F 273 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6623 (pp20) REVERT: F 280 VAL cc_start: 0.6506 (p) cc_final: 0.5562 (t) REVERT: F 324 CYS cc_start: 0.7361 (m) cc_final: 0.7096 (m) REVERT: F 327 GLU cc_start: 0.7314 (mp0) cc_final: 0.6560 (mp0) REVERT: F 348 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6345 (t80) REVERT: F 369 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7512 (ttp80) REVERT: F 379 ASP cc_start: 0.8385 (p0) cc_final: 0.7579 (p0) REVERT: F 383 ILE cc_start: 0.7928 (mt) cc_final: 0.7622 (mm) REVERT: F 386 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7175 (ptm) REVERT: F 514 ARG cc_start: 0.7068 (tpp80) cc_final: 0.6227 (tpp80) REVERT: F 517 LYS cc_start: 0.7532 (ptmt) cc_final: 0.7258 (pttt) REVERT: F 577 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7612 (t) REVERT: F 586 GLU cc_start: 0.7384 (tp30) cc_final: 0.7148 (tp30) REVERT: F 611 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7788 (pp) REVERT: F 640 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7982 (p) REVERT: G 141 MET cc_start: 0.5773 (tmm) cc_final: 0.5565 (tmm) REVERT: G 160 LYS cc_start: 0.8251 (ttmt) cc_final: 0.8009 (ttmt) REVERT: G 177 LYS cc_start: 0.8612 (tttm) cc_final: 0.8301 (tttm) REVERT: G 179 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6975 (tm-30) REVERT: G 189 LYS cc_start: 0.8400 (mttp) cc_final: 0.8116 (mttm) REVERT: G 191 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7824 (t) REVERT: G 231 GLU cc_start: 0.6869 (tp30) cc_final: 0.6664 (mm-30) REVERT: G 249 ILE cc_start: 0.8243 (mt) cc_final: 0.7931 (pt) REVERT: G 300 MET cc_start: 0.6476 (mmm) cc_final: 0.6047 (mmm) REVERT: G 302 ARG cc_start: 0.7257 (mmt180) cc_final: 0.6995 (mmt180) REVERT: G 323 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.7985 (p) REVERT: G 324 GLU cc_start: 0.7459 (tm-30) cc_final: 0.6992 (tm-30) REVERT: G 352 LYS cc_start: 0.7212 (tptt) cc_final: 0.6816 (tptt) REVERT: G 361 THR cc_start: 0.6398 (OUTLIER) cc_final: 0.5752 (m) REVERT: G 396 ILE cc_start: 0.8181 (tp) cc_final: 0.7945 (tp) REVERT: G 441 ASP cc_start: 0.7608 (t0) cc_final: 0.7195 (t0) REVERT: G 452 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.6672 (ttp80) REVERT: G 453 GLU cc_start: 0.6861 (mp0) cc_final: 0.5883 (mp0) REVERT: G 466 LYS cc_start: 0.7913 (tptm) cc_final: 0.7566 (mmmm) REVERT: G 485 LEU cc_start: 0.8309 (tp) cc_final: 0.7965 (tt) REVERT: G 494 MET cc_start: 0.7798 (tmm) cc_final: 0.7577 (tmm) REVERT: H 11 LYS cc_start: 0.8188 (tptp) cc_final: 0.7946 (tptp) REVERT: H 26 LEU cc_start: 0.8602 (tp) cc_final: 0.8359 (tp) REVERT: H 32 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6726 (mm-30) REVERT: H 35 ARG cc_start: 0.6878 (mtm-85) cc_final: 0.6647 (mtm-85) REVERT: H 36 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6716 (tm-30) REVERT: H 43 GLU cc_start: 0.7317 (mp0) cc_final: 0.6891 (mp0) REVERT: H 48 ILE cc_start: 0.8595 (mt) cc_final: 0.8286 (mp) REVERT: H 119 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6499 (mm-30) REVERT: H 133 MET cc_start: 0.7559 (tmm) cc_final: 0.7215 (tmm) REVERT: I 13 THR cc_start: 0.8535 (p) cc_final: 0.8205 (p) REVERT: I 75 SER cc_start: 0.8129 (t) cc_final: 0.7663 (p) REVERT: I 80 ASP cc_start: 0.7026 (m-30) cc_final: 0.6717 (m-30) REVERT: I 128 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7554 (mmmt) REVERT: I 139 TYR cc_start: 0.7811 (m-80) cc_final: 0.7210 (m-80) REVERT: I 145 LYS cc_start: 0.8003 (mttt) cc_final: 0.7738 (mttp) REVERT: I 151 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7244 (tttp) REVERT: I 200 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6827 (tm-30) REVERT: I 202 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8138 (mm) REVERT: I 258 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7989 (ttmt) REVERT: I 332 TYR cc_start: 0.8072 (t80) cc_final: 0.7790 (t80) REVERT: I 346 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6891 (mt-10) REVERT: I 389 GLU cc_start: 0.7171 (tp30) cc_final: 0.6907 (tp30) REVERT: I 405 ASN cc_start: 0.7904 (m-40) cc_final: 0.7519 (m-40) REVERT: I 414 GLU cc_start: 0.7273 (tt0) cc_final: 0.6930 (mt-10) REVERT: I 442 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.6326 (m-30) REVERT: J 84 ASP cc_start: 0.7568 (m-30) cc_final: 0.7094 (m-30) REVERT: J 137 ASP cc_start: 0.6485 (p0) cc_final: 0.6255 (p0) outliers start: 177 outliers final: 113 residues processed: 1112 average time/residue: 0.5043 time to fit residues: 852.7627 Evaluate side-chains 1133 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 998 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 628 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 10 TRP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 577 SER Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 621 TRP Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 640 THR Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 193 CYS Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 372 ILE Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 525 HIS Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 442 ASP Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 154 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 5.9990 chunk 320 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 356 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 112 GLN A 118 HIS ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN E 34 ASN E 116 ASN F 53 GLN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS J 34 ASN J 116 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 29856 Z= 0.377 Angle : 0.696 12.516 40460 Z= 0.353 Chirality : 0.050 0.418 4532 Planarity : 0.005 0.089 5202 Dihedral : 6.666 59.726 4132 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 5.65 % Allowed : 23.39 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.35 (0.13), residues: 3712 helix: -0.38 (0.13), residues: 1482 sheet: -2.54 (0.25), residues: 368 loop : -2.38 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP I 271 HIS 0.007 0.001 HIS F 165 PHE 0.031 0.002 PHE G 518 TYR 0.019 0.002 TYR J 145 ARG 0.011 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1033 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7397 (mmmt) REVERT: A 61 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8337 (pt) REVERT: A 83 ASP cc_start: 0.7393 (t0) cc_final: 0.6958 (t0) REVERT: A 86 ARG cc_start: 0.7824 (ttt-90) cc_final: 0.7579 (ttt-90) REVERT: A 142 MET cc_start: 0.7523 (ttt) cc_final: 0.7211 (ttp) REVERT: A 156 ARG cc_start: 0.7525 (mmt180) cc_final: 0.6494 (mtt180) REVERT: A 171 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7279 (ttm-80) REVERT: A 175 GLN cc_start: 0.8018 (mp10) cc_final: 0.7646 (mp10) REVERT: A 184 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7905 (mttm) REVERT: A 232 CYS cc_start: 0.5384 (OUTLIER) cc_final: 0.5036 (p) REVERT: A 239 LYS cc_start: 0.8019 (tttp) cc_final: 0.7731 (tttp) REVERT: A 243 ARG cc_start: 0.7710 (ttt180) cc_final: 0.7418 (ttt180) REVERT: A 251 GLU cc_start: 0.7036 (pt0) cc_final: 0.6762 (pt0) REVERT: A 273 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6685 (pp20) REVERT: A 327 GLU cc_start: 0.7334 (mp0) cc_final: 0.6535 (mp0) REVERT: A 328 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7273 (mt-10) REVERT: A 346 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: A 369 ARG cc_start: 0.7761 (ttt180) cc_final: 0.7433 (ttt180) REVERT: A 379 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.7705 (p0) REVERT: A 382 LEU cc_start: 0.7565 (tp) cc_final: 0.7197 (tt) REVERT: A 383 ILE cc_start: 0.7962 (mt) cc_final: 0.7543 (mp) REVERT: A 447 GLU cc_start: 0.7467 (tm-30) cc_final: 0.6873 (tm-30) REVERT: A 514 ARG cc_start: 0.7306 (tpp80) cc_final: 0.6726 (tpp80) REVERT: A 517 LYS cc_start: 0.7831 (ptmt) cc_final: 0.7568 (ptmt) REVERT: A 604 LYS cc_start: 0.8523 (mmmm) cc_final: 0.8177 (mmtp) REVERT: A 613 ASP cc_start: 0.7436 (m-30) cc_final: 0.7194 (m-30) REVERT: A 632 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6346 (tp30) REVERT: A 649 LYS cc_start: 0.2944 (OUTLIER) cc_final: 0.2645 (pttm) REVERT: B 160 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8265 (ttmt) REVERT: B 176 LEU cc_start: 0.8261 (tt) cc_final: 0.8036 (tt) REVERT: B 179 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7099 (tm-30) REVERT: B 182 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7688 (mtpt) REVERT: B 291 MET cc_start: 0.7161 (mtm) cc_final: 0.6581 (mtm) REVERT: B 295 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7006 (mt-10) REVERT: B 302 ARG cc_start: 0.7311 (mmt180) cc_final: 0.6883 (mmt180) REVERT: B 324 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 349 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6986 (ttpt) REVERT: B 352 LYS cc_start: 0.7537 (tptt) cc_final: 0.7119 (tptt) REVERT: B 361 THR cc_start: 0.6695 (OUTLIER) cc_final: 0.6160 (m) REVERT: B 396 ILE cc_start: 0.8076 (tp) cc_final: 0.7828 (tp) REVERT: B 441 ASP cc_start: 0.7934 (t0) cc_final: 0.7641 (t0) REVERT: B 453 GLU cc_start: 0.6951 (mp0) cc_final: 0.6277 (mp0) REVERT: B 457 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7393 (ttmt) REVERT: B 466 LYS cc_start: 0.8012 (tptm) cc_final: 0.7269 (mmmm) REVERT: B 474 LYS cc_start: 0.7661 (ttpt) cc_final: 0.7459 (ttpt) REVERT: B 494 MET cc_start: 0.7801 (tmm) cc_final: 0.7562 (tmm) REVERT: C 11 LYS cc_start: 0.8031 (tptp) cc_final: 0.7710 (tptp) REVERT: C 100 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7888 (mmmm) REVERT: C 119 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6596 (mm-30) REVERT: D 52 ASP cc_start: 0.7315 (t0) cc_final: 0.7093 (t0) REVERT: D 80 ASP cc_start: 0.7033 (m-30) cc_final: 0.6742 (m-30) REVERT: D 93 LYS cc_start: 0.8417 (mttp) cc_final: 0.8072 (mttt) REVERT: D 114 LEU cc_start: 0.7618 (mt) cc_final: 0.7328 (mt) REVERT: D 128 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7642 (mmmt) REVERT: D 139 TYR cc_start: 0.7994 (m-80) cc_final: 0.7215 (m-80) REVERT: D 151 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7637 (mtpp) REVERT: D 251 ILE cc_start: 0.8568 (mp) cc_final: 0.8335 (mt) REVERT: D 343 GLU cc_start: 0.6916 (tt0) cc_final: 0.6634 (tt0) REVERT: D 346 GLU cc_start: 0.7209 (tt0) cc_final: 0.6941 (mt-10) REVERT: D 389 GLU cc_start: 0.7205 (tp30) cc_final: 0.6950 (tp30) REVERT: D 414 GLU cc_start: 0.7217 (tt0) cc_final: 0.6822 (mt-10) REVERT: E 38 LEU cc_start: 0.8516 (mm) cc_final: 0.8163 (mp) REVERT: E 84 ASP cc_start: 0.7702 (m-30) cc_final: 0.7123 (m-30) REVERT: F 7 THR cc_start: 0.8215 (m) cc_final: 0.7912 (t) REVERT: F 14 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7388 (mmmt) REVERT: F 44 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7601 (mp) REVERT: F 60 MET cc_start: 0.7584 (ptp) cc_final: 0.7150 (mtm) REVERT: F 83 ASP cc_start: 0.7318 (t0) cc_final: 0.6864 (t0) REVERT: F 86 ARG cc_start: 0.7739 (ttt-90) cc_final: 0.7484 (ttt-90) REVERT: F 119 GLU cc_start: 0.7125 (mp0) cc_final: 0.6763 (mp0) REVERT: F 133 GLU cc_start: 0.6889 (pp20) cc_final: 0.6454 (pp20) REVERT: F 142 MET cc_start: 0.7319 (ttt) cc_final: 0.7085 (ttp) REVERT: F 156 ARG cc_start: 0.7496 (mmt180) cc_final: 0.6409 (mtt180) REVERT: F 175 GLN cc_start: 0.8002 (mp10) cc_final: 0.7625 (mp10) REVERT: F 184 LYS cc_start: 0.8222 (mmtt) cc_final: 0.8014 (mmtm) REVERT: F 232 CYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5719 (p) REVERT: F 251 GLU cc_start: 0.7094 (pt0) cc_final: 0.6831 (pt0) REVERT: F 273 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6577 (pp20) REVERT: F 276 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6461 (mm-30) REVERT: F 280 VAL cc_start: 0.6917 (p) cc_final: 0.6085 (t) REVERT: F 327 GLU cc_start: 0.7421 (mp0) cc_final: 0.7183 (mm-30) REVERT: F 345 ILE cc_start: 0.8261 (pt) cc_final: 0.7918 (mt) REVERT: F 348 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6523 (t80) REVERT: F 379 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7637 (p0) REVERT: F 383 ILE cc_start: 0.7981 (mt) cc_final: 0.7622 (mp) REVERT: F 386 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7238 (ptm) REVERT: F 514 ARG cc_start: 0.7125 (tpp80) cc_final: 0.6262 (tpp80) REVERT: F 517 LYS cc_start: 0.7611 (ptmt) cc_final: 0.7286 (pttt) REVERT: F 577 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7736 (t) REVERT: F 586 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7188 (tp30) REVERT: F 611 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7746 (pp) REVERT: F 640 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.8014 (p) REVERT: G 160 LYS cc_start: 0.8351 (ttmt) cc_final: 0.8090 (ttmt) REVERT: G 179 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7107 (tm-30) REVERT: G 189 LYS cc_start: 0.8420 (mttp) cc_final: 0.8163 (mttm) REVERT: G 191 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7827 (t) REVERT: G 206 ARG cc_start: 0.7261 (ttm170) cc_final: 0.6983 (ttm170) REVERT: G 323 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8042 (p) REVERT: G 324 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7118 (tm-30) REVERT: G 352 LYS cc_start: 0.7418 (tptt) cc_final: 0.6931 (tptt) REVERT: G 385 ILE cc_start: 0.8440 (mm) cc_final: 0.8170 (mm) REVERT: G 396 ILE cc_start: 0.8159 (tp) cc_final: 0.7891 (tp) REVERT: G 453 GLU cc_start: 0.6905 (mp0) cc_final: 0.6043 (mp0) REVERT: G 462 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7964 (ttp80) REVERT: G 466 LYS cc_start: 0.7963 (tptm) cc_final: 0.7575 (ttmt) REVERT: G 494 MET cc_start: 0.7838 (tmm) cc_final: 0.7602 (tmm) REVERT: H 11 LYS cc_start: 0.8194 (tptp) cc_final: 0.7963 (tptp) REVERT: H 13 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8189 (mtpp) REVERT: H 36 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6800 (tm-30) REVERT: H 43 GLU cc_start: 0.7356 (mp0) cc_final: 0.6946 (mp0) REVERT: H 56 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8122 (mtmm) REVERT: H 119 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6420 (mm-30) REVERT: H 133 MET cc_start: 0.7729 (tmm) cc_final: 0.7420 (tmm) REVERT: H 154 LYS cc_start: 0.8162 (tmtt) cc_final: 0.7840 (tmtt) REVERT: I 13 THR cc_start: 0.8501 (p) cc_final: 0.8166 (p) REVERT: I 18 HIS cc_start: 0.8282 (m90) cc_final: 0.7983 (m170) REVERT: I 80 ASP cc_start: 0.7074 (m-30) cc_final: 0.6791 (m-30) REVERT: I 128 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7599 (mmmt) REVERT: I 139 TYR cc_start: 0.7972 (m-80) cc_final: 0.7208 (m-80) REVERT: I 145 LYS cc_start: 0.8226 (mttt) cc_final: 0.7902 (mttp) REVERT: I 151 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7392 (tttp) REVERT: I 200 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6865 (tm-30) REVERT: I 332 TYR cc_start: 0.8164 (t80) cc_final: 0.7883 (t80) REVERT: I 346 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: I 389 GLU cc_start: 0.7271 (tp30) cc_final: 0.7021 (tp30) REVERT: I 414 GLU cc_start: 0.7287 (tt0) cc_final: 0.6945 (mt-10) REVERT: I 448 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8459 (p) REVERT: J 34 ASN cc_start: 0.8335 (m-40) cc_final: 0.8076 (m110) REVERT: J 38 LEU cc_start: 0.8533 (mm) cc_final: 0.8186 (mp) REVERT: J 84 ASP cc_start: 0.7642 (m-30) cc_final: 0.7139 (m-30) REVERT: J 137 ASP cc_start: 0.6582 (p0) cc_final: 0.6355 (p0) outliers start: 177 outliers final: 118 residues processed: 1115 average time/residue: 0.4639 time to fit residues: 775.9930 Evaluate side-chains 1157 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1013 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 577 SER Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 640 THR Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 668 ARG Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 193 CYS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 372 ILE Chi-restraints excluded: chain G residue 410 ASP Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 525 HIS Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 346 GLU Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain I residue 364 LYS Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 260 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 299 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 354 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 216 optimal weight: 0.3980 chunk 163 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 397 ASN D 405 ASN E 34 ASN E 116 ASN F 53 GLN F 145 HIS ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** G 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 ASN J 116 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29856 Z= 0.221 Angle : 0.663 12.407 40460 Z= 0.334 Chirality : 0.046 0.275 4532 Planarity : 0.005 0.083 5202 Dihedral : 6.510 58.448 4132 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 5.39 % Allowed : 24.57 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.19 (0.13), residues: 3712 helix: -0.20 (0.14), residues: 1494 sheet: -2.38 (0.25), residues: 376 loop : -2.35 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 339 HIS 0.006 0.001 HIS A 165 PHE 0.027 0.001 PHE A 572 TYR 0.016 0.001 TYR A 400 ARG 0.010 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1026 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8317 (tttt) REVERT: A 14 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7401 (mmmt) REVERT: A 80 LYS cc_start: 0.8111 (tttm) cc_final: 0.7788 (tttt) REVERT: A 83 ASP cc_start: 0.7345 (t0) cc_final: 0.6938 (t0) REVERT: A 86 ARG cc_start: 0.7804 (ttt-90) cc_final: 0.7570 (ttt-90) REVERT: A 120 MET cc_start: 0.8019 (ttp) cc_final: 0.7810 (ttm) REVERT: A 142 MET cc_start: 0.7482 (ttt) cc_final: 0.7181 (ttp) REVERT: A 156 ARG cc_start: 0.7500 (mmt180) cc_final: 0.6466 (mtt180) REVERT: A 175 GLN cc_start: 0.7967 (mp10) cc_final: 0.7599 (mp10) REVERT: A 184 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7908 (mttm) REVERT: A 232 CYS cc_start: 0.5367 (OUTLIER) cc_final: 0.5028 (p) REVERT: A 239 LYS cc_start: 0.7971 (tttp) cc_final: 0.7663 (tttp) REVERT: A 243 ARG cc_start: 0.7693 (ttt180) cc_final: 0.7385 (ttt180) REVERT: A 251 GLU cc_start: 0.7002 (pt0) cc_final: 0.6736 (pt0) REVERT: A 273 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6599 (pp20) REVERT: A 327 GLU cc_start: 0.7296 (mp0) cc_final: 0.6500 (mp0) REVERT: A 328 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7279 (mt-10) REVERT: A 346 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7041 (m-30) REVERT: A 379 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.7654 (p0) REVERT: A 383 ILE cc_start: 0.7880 (mt) cc_final: 0.7529 (mp) REVERT: A 447 GLU cc_start: 0.7577 (tm-30) cc_final: 0.6907 (tm-30) REVERT: A 514 ARG cc_start: 0.7247 (tpp80) cc_final: 0.6732 (tpp80) REVERT: A 517 LYS cc_start: 0.7807 (ptmt) cc_final: 0.7590 (ptmt) REVERT: A 604 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8158 (mmtp) REVERT: A 611 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7875 (pp) REVERT: A 613 ASP cc_start: 0.7394 (m-30) cc_final: 0.7132 (m-30) REVERT: A 649 LYS cc_start: 0.2757 (OUTLIER) cc_final: 0.2481 (pttm) REVERT: B 160 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8202 (ttmt) REVERT: B 176 LEU cc_start: 0.8194 (tt) cc_final: 0.7983 (tt) REVERT: B 179 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7026 (tm-30) REVERT: B 291 MET cc_start: 0.7116 (mtm) cc_final: 0.6554 (mtm) REVERT: B 295 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6980 (mt-10) REVERT: B 302 ARG cc_start: 0.7289 (mmt180) cc_final: 0.6822 (mmt180) REVERT: B 324 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7026 (tm-30) REVERT: B 352 LYS cc_start: 0.7421 (tptt) cc_final: 0.7059 (tptt) REVERT: B 361 THR cc_start: 0.6530 (OUTLIER) cc_final: 0.5448 (m) REVERT: B 396 ILE cc_start: 0.8004 (tp) cc_final: 0.7753 (tp) REVERT: B 441 ASP cc_start: 0.7907 (t0) cc_final: 0.7590 (t0) REVERT: B 444 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7599 (tttt) REVERT: B 453 GLU cc_start: 0.6954 (mp0) cc_final: 0.6238 (mp0) REVERT: B 457 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7277 (ttmt) REVERT: B 494 MET cc_start: 0.7787 (tmm) cc_final: 0.7551 (tmm) REVERT: C 11 LYS cc_start: 0.7975 (tptp) cc_final: 0.7643 (tptp) REVERT: C 100 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7862 (mmmm) REVERT: C 118 LEU cc_start: 0.7824 (tp) cc_final: 0.7017 (tp) REVERT: C 119 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6550 (mm-30) REVERT: D 52 ASP cc_start: 0.7379 (t0) cc_final: 0.7144 (t0) REVERT: D 80 ASP cc_start: 0.7001 (m-30) cc_final: 0.6700 (m-30) REVERT: D 93 LYS cc_start: 0.8386 (mttp) cc_final: 0.8052 (mttt) REVERT: D 114 LEU cc_start: 0.7624 (mt) cc_final: 0.7375 (mt) REVERT: D 118 ASP cc_start: 0.7638 (m-30) cc_final: 0.7417 (m-30) REVERT: D 128 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7638 (mmmt) REVERT: D 139 TYR cc_start: 0.7949 (m-80) cc_final: 0.7214 (m-80) REVERT: D 141 GLU cc_start: 0.7109 (pp20) cc_final: 0.6602 (pp20) REVERT: D 151 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7568 (mtpp) REVERT: D 251 ILE cc_start: 0.8562 (mp) cc_final: 0.8338 (mt) REVERT: D 343 GLU cc_start: 0.6912 (tt0) cc_final: 0.6624 (tt0) REVERT: D 346 GLU cc_start: 0.7161 (tt0) cc_final: 0.6892 (mt-10) REVERT: D 389 GLU cc_start: 0.7150 (tp30) cc_final: 0.6867 (tp30) REVERT: D 414 GLU cc_start: 0.7192 (tt0) cc_final: 0.6806 (mt-10) REVERT: E 35 VAL cc_start: 0.8283 (p) cc_final: 0.8070 (p) REVERT: E 38 LEU cc_start: 0.8368 (mm) cc_final: 0.8033 (mp) REVERT: E 84 ASP cc_start: 0.7594 (m-30) cc_final: 0.7012 (m-30) REVERT: F 7 THR cc_start: 0.8169 (m) cc_final: 0.7894 (t) REVERT: F 14 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7391 (mmmt) REVERT: F 80 LYS cc_start: 0.8122 (tttm) cc_final: 0.7804 (tttt) REVERT: F 83 ASP cc_start: 0.7261 (t0) cc_final: 0.6841 (t0) REVERT: F 86 ARG cc_start: 0.7723 (ttt-90) cc_final: 0.7447 (ttt-90) REVERT: F 117 GLU cc_start: 0.7447 (tt0) cc_final: 0.6855 (tt0) REVERT: F 119 GLU cc_start: 0.7153 (mp0) cc_final: 0.6720 (mp0) REVERT: F 120 MET cc_start: 0.7904 (ttp) cc_final: 0.7645 (ttm) REVERT: F 133 GLU cc_start: 0.6796 (pp20) cc_final: 0.6336 (pp20) REVERT: F 138 ASP cc_start: 0.7883 (t0) cc_final: 0.7608 (t0) REVERT: F 142 MET cc_start: 0.7304 (ttt) cc_final: 0.7073 (ttp) REVERT: F 156 ARG cc_start: 0.7470 (mmt180) cc_final: 0.6463 (mtt180) REVERT: F 172 ARG cc_start: 0.7788 (ptm160) cc_final: 0.7228 (ptm160) REVERT: F 174 TRP cc_start: 0.7987 (t60) cc_final: 0.7724 (t60) REVERT: F 175 GLN cc_start: 0.7913 (mp10) cc_final: 0.7597 (mp10) REVERT: F 177 LYS cc_start: 0.8521 (ttpp) cc_final: 0.8091 (ttmm) REVERT: F 232 CYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5817 (p) REVERT: F 251 GLU cc_start: 0.7058 (pt0) cc_final: 0.6790 (pt0) REVERT: F 273 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6574 (pp20) REVERT: F 276 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6422 (mm-30) REVERT: F 327 GLU cc_start: 0.7377 (mp0) cc_final: 0.7162 (mm-30) REVERT: F 328 GLU cc_start: 0.7872 (mt-10) cc_final: 0.6919 (mt-10) REVERT: F 348 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6382 (t80) REVERT: F 369 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7497 (ttp80) REVERT: F 379 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7242 (p0) REVERT: F 383 ILE cc_start: 0.7972 (mt) cc_final: 0.7621 (mp) REVERT: F 447 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6755 (tt0) REVERT: F 577 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7707 (t) REVERT: F 586 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: F 604 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8180 (mmtp) REVERT: F 611 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7765 (pp) REVERT: F 640 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.8016 (p) REVERT: G 145 LYS cc_start: 0.7254 (pttt) cc_final: 0.6914 (pttt) REVERT: G 160 LYS cc_start: 0.8295 (ttmt) cc_final: 0.8045 (ttmt) REVERT: G 179 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6998 (tm-30) REVERT: G 189 LYS cc_start: 0.8405 (mttp) cc_final: 0.8135 (mttm) REVERT: G 191 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7850 (t) REVERT: G 237 ARG cc_start: 0.7414 (mtp85) cc_final: 0.6960 (mtp85) REVERT: G 295 GLU cc_start: 0.7235 (mt-10) cc_final: 0.7008 (mt-10) REVERT: G 323 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.7975 (p) REVERT: G 324 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7064 (tm-30) REVERT: G 352 LYS cc_start: 0.7337 (tptt) cc_final: 0.6865 (tptt) REVERT: G 385 ILE cc_start: 0.8391 (mm) cc_final: 0.8112 (mm) REVERT: G 396 ILE cc_start: 0.8173 (tp) cc_final: 0.7893 (tp) REVERT: G 453 GLU cc_start: 0.6876 (mp0) cc_final: 0.6053 (mp0) REVERT: G 462 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7892 (ttp80) REVERT: G 466 LYS cc_start: 0.7869 (tptm) cc_final: 0.7555 (mmmm) REVERT: G 485 LEU cc_start: 0.8318 (tp) cc_final: 0.8014 (tt) REVERT: G 487 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8226 (mtmm) REVERT: G 494 MET cc_start: 0.7833 (tmm) cc_final: 0.7606 (tmm) REVERT: H 11 LYS cc_start: 0.8162 (tptp) cc_final: 0.7902 (tptp) REVERT: H 32 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6859 (mm-30) REVERT: H 36 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6782 (tm-30) REVERT: H 48 ILE cc_start: 0.8641 (mt) cc_final: 0.8304 (mp) REVERT: H 119 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6307 (mm-30) REVERT: H 133 MET cc_start: 0.7533 (tmm) cc_final: 0.7203 (tmm) REVERT: I 13 THR cc_start: 0.8511 (p) cc_final: 0.7998 (p) REVERT: I 80 ASP cc_start: 0.7038 (m-30) cc_final: 0.6744 (m-30) REVERT: I 128 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7585 (mmmt) REVERT: I 139 TYR cc_start: 0.7930 (m-80) cc_final: 0.7176 (m-80) REVERT: I 145 LYS cc_start: 0.8146 (mttt) cc_final: 0.7865 (mttp) REVERT: I 151 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7334 (tttp) REVERT: I 200 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6874 (tm-30) REVERT: I 202 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8173 (mm) REVERT: I 332 TYR cc_start: 0.8112 (t80) cc_final: 0.7709 (t80) REVERT: I 346 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: I 389 GLU cc_start: 0.7185 (tp30) cc_final: 0.6899 (tp30) REVERT: I 405 ASN cc_start: 0.7879 (m-40) cc_final: 0.7614 (m-40) REVERT: I 414 GLU cc_start: 0.7262 (tt0) cc_final: 0.6947 (mt-10) REVERT: I 448 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8500 (p) REVERT: J 34 ASN cc_start: 0.8342 (m-40) cc_final: 0.8044 (m110) REVERT: J 38 LEU cc_start: 0.8457 (mm) cc_final: 0.8150 (mp) REVERT: J 44 ASP cc_start: 0.7243 (m-30) cc_final: 0.6766 (m-30) REVERT: J 84 ASP cc_start: 0.7559 (m-30) cc_final: 0.7051 (m-30) REVERT: J 137 ASP cc_start: 0.6496 (p0) cc_final: 0.6282 (p0) outliers start: 169 outliers final: 113 residues processed: 1108 average time/residue: 0.5096 time to fit residues: 859.3818 Evaluate side-chains 1136 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1000 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 628 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 10 TRP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 577 SER Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 640 THR Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 668 ARG Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 193 CYS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 372 ILE Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 410 ASP Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 525 HIS Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 346 GLU Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain I residue 364 LYS Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 397 ASN D 405 ASN E 116 ASN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** I 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29856 Z= 0.257 Angle : 0.684 11.682 40460 Z= 0.342 Chirality : 0.047 0.263 4532 Planarity : 0.005 0.083 5202 Dihedral : 6.505 59.118 4132 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 5.30 % Allowed : 24.95 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.15 (0.13), residues: 3712 helix: -0.21 (0.14), residues: 1494 sheet: -2.46 (0.26), residues: 372 loop : -2.27 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 271 HIS 0.006 0.001 HIS A 165 PHE 0.029 0.001 PHE A 572 TYR 0.019 0.001 TYR A 400 ARG 0.010 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1012 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8313 (tttt) REVERT: A 14 LYS cc_start: 0.7648 (mmmt) cc_final: 0.7392 (mmmt) REVERT: A 61 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8415 (pt) REVERT: A 80 LYS cc_start: 0.8126 (tttm) cc_final: 0.7794 (tttt) REVERT: A 83 ASP cc_start: 0.7355 (t0) cc_final: 0.6948 (t0) REVERT: A 86 ARG cc_start: 0.7829 (ttt-90) cc_final: 0.7579 (ttt-90) REVERT: A 120 MET cc_start: 0.8013 (ttp) cc_final: 0.7809 (ttm) REVERT: A 142 MET cc_start: 0.7507 (ttt) cc_final: 0.7207 (ttp) REVERT: A 156 ARG cc_start: 0.7516 (mmt180) cc_final: 0.6471 (mtt180) REVERT: A 175 GLN cc_start: 0.7934 (mp10) cc_final: 0.7654 (mp10) REVERT: A 184 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7910 (mttm) REVERT: A 232 CYS cc_start: 0.5391 (OUTLIER) cc_final: 0.4988 (p) REVERT: A 239 LYS cc_start: 0.8011 (tttp) cc_final: 0.7695 (tttp) REVERT: A 243 ARG cc_start: 0.7702 (ttt180) cc_final: 0.7392 (ttt180) REVERT: A 251 GLU cc_start: 0.7006 (pt0) cc_final: 0.6737 (pt0) REVERT: A 273 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6618 (pp20) REVERT: A 327 GLU cc_start: 0.7312 (mp0) cc_final: 0.6518 (mp0) REVERT: A 328 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7271 (mt-10) REVERT: A 346 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: A 369 ARG cc_start: 0.7944 (ttt90) cc_final: 0.7548 (ttp80) REVERT: A 379 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7636 (p0) REVERT: A 383 ILE cc_start: 0.7828 (mt) cc_final: 0.7471 (mp) REVERT: A 386 MET cc_start: 0.7582 (ptm) cc_final: 0.7372 (ptp) REVERT: A 440 LYS cc_start: 0.5772 (OUTLIER) cc_final: 0.5360 (mtmm) REVERT: A 447 GLU cc_start: 0.7556 (tm-30) cc_final: 0.6872 (tm-30) REVERT: A 514 ARG cc_start: 0.7235 (tpp80) cc_final: 0.6747 (tpp80) REVERT: A 517 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7569 (ptmt) REVERT: A 604 LYS cc_start: 0.8446 (mmmm) cc_final: 0.8177 (mmtp) REVERT: A 611 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7877 (pp) REVERT: A 613 ASP cc_start: 0.7423 (m-30) cc_final: 0.7134 (m-30) REVERT: A 632 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6655 (tp30) REVERT: A 649 LYS cc_start: 0.2311 (OUTLIER) cc_final: 0.1988 (pttm) REVERT: B 143 LEU cc_start: 0.7526 (tp) cc_final: 0.7267 (tp) REVERT: B 160 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8217 (ttmt) REVERT: B 176 LEU cc_start: 0.8216 (tt) cc_final: 0.8006 (tt) REVERT: B 179 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7034 (tm-30) REVERT: B 206 ARG cc_start: 0.7233 (ttm170) cc_final: 0.7021 (ttm170) REVERT: B 221 THR cc_start: 0.6680 (p) cc_final: 0.6294 (p) REVERT: B 291 MET cc_start: 0.7123 (mtm) cc_final: 0.6566 (mtm) REVERT: B 295 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7003 (mt-10) REVERT: B 302 ARG cc_start: 0.7288 (mmt180) cc_final: 0.6810 (mmt180) REVERT: B 324 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7026 (tm-30) REVERT: B 352 LYS cc_start: 0.7419 (tptt) cc_final: 0.7061 (tptt) REVERT: B 361 THR cc_start: 0.6521 (OUTLIER) cc_final: 0.5503 (m) REVERT: B 396 ILE cc_start: 0.8014 (tp) cc_final: 0.7765 (tp) REVERT: B 441 ASP cc_start: 0.7925 (t0) cc_final: 0.7659 (t0) REVERT: B 444 LYS cc_start: 0.8037 (tmtt) cc_final: 0.7601 (tttt) REVERT: B 453 GLU cc_start: 0.6967 (mp0) cc_final: 0.6247 (mp0) REVERT: B 457 LYS cc_start: 0.7832 (ttmt) cc_final: 0.7304 (ttmt) REVERT: B 466 LYS cc_start: 0.7976 (tptm) cc_final: 0.7718 (ttmm) REVERT: B 494 MET cc_start: 0.7800 (tmm) cc_final: 0.7556 (tmm) REVERT: C 11 LYS cc_start: 0.7936 (tptp) cc_final: 0.7642 (tptp) REVERT: C 100 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7853 (mmmm) REVERT: C 118 LEU cc_start: 0.7814 (tp) cc_final: 0.7013 (tp) REVERT: C 119 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6552 (mm-30) REVERT: D 52 ASP cc_start: 0.7374 (t0) cc_final: 0.7140 (t0) REVERT: D 80 ASP cc_start: 0.7019 (m-30) cc_final: 0.6714 (m-30) REVERT: D 93 LYS cc_start: 0.8370 (mttp) cc_final: 0.8035 (mttt) REVERT: D 139 TYR cc_start: 0.7996 (m-80) cc_final: 0.7176 (m-80) REVERT: D 141 GLU cc_start: 0.7111 (pp20) cc_final: 0.6614 (pp20) REVERT: D 151 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7612 (mtpp) REVERT: D 251 ILE cc_start: 0.8556 (mp) cc_final: 0.8335 (mt) REVERT: D 346 GLU cc_start: 0.7176 (tt0) cc_final: 0.6906 (mt-10) REVERT: D 389 GLU cc_start: 0.7161 (tp30) cc_final: 0.6875 (tp30) REVERT: D 414 GLU cc_start: 0.7200 (tt0) cc_final: 0.6814 (mt-10) REVERT: E 35 VAL cc_start: 0.8388 (p) cc_final: 0.8183 (p) REVERT: E 84 ASP cc_start: 0.7636 (m-30) cc_final: 0.7005 (m-30) REVERT: F 7 THR cc_start: 0.8174 (m) cc_final: 0.7900 (t) REVERT: F 14 LYS cc_start: 0.7722 (mmmt) cc_final: 0.7401 (mmmt) REVERT: F 44 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7570 (mp) REVERT: F 80 LYS cc_start: 0.8124 (tttm) cc_final: 0.7788 (tttt) REVERT: F 83 ASP cc_start: 0.7278 (t0) cc_final: 0.6850 (t0) REVERT: F 86 ARG cc_start: 0.7719 (ttt-90) cc_final: 0.7471 (ttt-90) REVERT: F 119 GLU cc_start: 0.7153 (mp0) cc_final: 0.6697 (mp0) REVERT: F 133 GLU cc_start: 0.6859 (pp20) cc_final: 0.6404 (pp20) REVERT: F 138 ASP cc_start: 0.7890 (t0) cc_final: 0.7615 (t0) REVERT: F 142 MET cc_start: 0.7336 (ttt) cc_final: 0.7100 (ttp) REVERT: F 156 ARG cc_start: 0.7478 (mmt180) cc_final: 0.6432 (mtt180) REVERT: F 172 ARG cc_start: 0.7812 (ptm160) cc_final: 0.7232 (ptm160) REVERT: F 174 TRP cc_start: 0.7965 (t60) cc_final: 0.7688 (t60) REVERT: F 175 GLN cc_start: 0.7937 (mp10) cc_final: 0.7630 (mp10) REVERT: F 232 CYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5846 (p) REVERT: F 237 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8373 (mtpt) REVERT: F 251 GLU cc_start: 0.7065 (pt0) cc_final: 0.6802 (pt0) REVERT: F 273 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6588 (pp20) REVERT: F 327 GLU cc_start: 0.7387 (mp0) cc_final: 0.7183 (mm-30) REVERT: F 328 GLU cc_start: 0.7889 (mt-10) cc_final: 0.6936 (mt-10) REVERT: F 348 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6433 (t80) REVERT: F 369 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7490 (ttp80) REVERT: F 379 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7588 (p0) REVERT: F 383 ILE cc_start: 0.7983 (mt) cc_final: 0.7621 (mp) REVERT: F 447 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6840 (tt0) REVERT: F 577 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7689 (t) REVERT: F 586 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7115 (tp30) REVERT: F 611 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7793 (pp) REVERT: F 640 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.8005 (p) REVERT: F 667 GLU cc_start: 0.7321 (mp0) cc_final: 0.7090 (mp0) REVERT: G 160 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8074 (ttmt) REVERT: G 177 LYS cc_start: 0.8675 (tttm) cc_final: 0.8345 (tttm) REVERT: G 179 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7016 (tm-30) REVERT: G 189 LYS cc_start: 0.8406 (mttp) cc_final: 0.8153 (mttm) REVERT: G 191 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7829 (t) REVERT: G 237 ARG cc_start: 0.7459 (mtp85) cc_final: 0.6955 (mtp85) REVERT: G 291 MET cc_start: 0.7229 (mtm) cc_final: 0.6681 (mtm) REVERT: G 295 GLU cc_start: 0.7244 (mt-10) cc_final: 0.7009 (mt-10) REVERT: G 323 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.7970 (p) REVERT: G 324 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7054 (tm-30) REVERT: G 352 LYS cc_start: 0.7348 (tptt) cc_final: 0.6878 (tptt) REVERT: G 385 ILE cc_start: 0.8424 (mm) cc_final: 0.8128 (mm) REVERT: G 396 ILE cc_start: 0.8206 (tp) cc_final: 0.7927 (tp) REVERT: G 453 GLU cc_start: 0.6877 (mp0) cc_final: 0.6044 (mp0) REVERT: G 466 LYS cc_start: 0.7901 (tptm) cc_final: 0.7601 (mmmm) REVERT: G 485 LEU cc_start: 0.8314 (tp) cc_final: 0.8005 (tt) REVERT: G 489 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7090 (tm-30) REVERT: G 494 MET cc_start: 0.7850 (tmm) cc_final: 0.7612 (tmm) REVERT: G 521 GLU cc_start: 0.7633 (tp30) cc_final: 0.7430 (tm-30) REVERT: H 11 LYS cc_start: 0.8145 (tptp) cc_final: 0.7875 (tptp) REVERT: H 36 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6791 (tm-30) REVERT: H 52 LEU cc_start: 0.8020 (mt) cc_final: 0.7785 (mp) REVERT: H 119 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6299 (mm-30) REVERT: H 133 MET cc_start: 0.7589 (tmm) cc_final: 0.7256 (tmm) REVERT: I 13 THR cc_start: 0.8490 (p) cc_final: 0.8165 (p) REVERT: I 18 HIS cc_start: 0.8360 (m170) cc_final: 0.8104 (m170) REVERT: I 80 ASP cc_start: 0.7044 (m-30) cc_final: 0.6760 (m-30) REVERT: I 128 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7589 (mmmt) REVERT: I 139 TYR cc_start: 0.7975 (m-80) cc_final: 0.7186 (m-80) REVERT: I 145 LYS cc_start: 0.8174 (mttt) cc_final: 0.7899 (mttp) REVERT: I 151 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7356 (tttp) REVERT: I 346 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6914 (mt-10) REVERT: I 389 GLU cc_start: 0.7181 (tp30) cc_final: 0.6917 (tp30) REVERT: I 414 GLU cc_start: 0.7264 (tt0) cc_final: 0.7038 (mt-10) REVERT: J 19 MET cc_start: 0.7676 (mmm) cc_final: 0.7419 (mmp) REVERT: J 34 ASN cc_start: 0.8336 (m-40) cc_final: 0.8054 (m110) REVERT: J 38 LEU cc_start: 0.8459 (mm) cc_final: 0.8066 (mp) REVERT: J 84 ASP cc_start: 0.7537 (m-30) cc_final: 0.7012 (m-30) REVERT: J 106 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: J 137 ASP cc_start: 0.6527 (p0) cc_final: 0.6317 (p0) outliers start: 166 outliers final: 124 residues processed: 1088 average time/residue: 0.4819 time to fit residues: 786.8162 Evaluate side-chains 1153 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1004 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 10 TRP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 577 SER Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 640 THR Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 668 ARG Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 193 CYS Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 372 ILE Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 410 ASP Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 525 HIS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 346 GLU Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain I residue 364 LYS Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 0.8980 chunk 339 optimal weight: 0.0870 chunk 310 optimal weight: 2.9990 chunk 330 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 298 optimal weight: 0.6980 chunk 312 optimal weight: 0.7980 chunk 329 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 405 ASN E 34 ASN E 116 ASN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** I 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29856 Z= 0.212 Angle : 0.677 11.859 40460 Z= 0.338 Chirality : 0.046 0.247 4532 Planarity : 0.005 0.085 5202 Dihedral : 6.292 57.569 4130 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.72 % Allowed : 25.75 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % 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: -2.02 (0.13), residues: 3712 helix: -0.05 (0.14), residues: 1486 sheet: -2.37 (0.25), residues: 392 loop : -2.23 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 271 HIS 0.006 0.001 HIS F 165 PHE 0.028 0.001 PHE A 572 TYR 0.018 0.001 TYR A 400 ARG 0.010 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 995 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8390 (tttt) REVERT: A 14 LYS cc_start: 0.7646 (mmmt) cc_final: 0.7386 (mmmt) REVERT: A 61 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8422 (pt) REVERT: A 80 LYS cc_start: 0.8100 (tttm) cc_final: 0.7771 (tttt) REVERT: A 83 ASP cc_start: 0.7333 (t0) cc_final: 0.6940 (t0) REVERT: A 86 ARG cc_start: 0.7822 (ttt-90) cc_final: 0.7594 (ttt-90) REVERT: A 120 MET cc_start: 0.8018 (ttp) cc_final: 0.7800 (ttm) REVERT: A 142 MET cc_start: 0.7507 (ttt) cc_final: 0.7198 (ttp) REVERT: A 156 ARG cc_start: 0.7494 (mmt180) cc_final: 0.6453 (mtt180) REVERT: A 184 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7864 (mttm) REVERT: A 232 CYS cc_start: 0.5348 (OUTLIER) cc_final: 0.4939 (p) REVERT: A 239 LYS cc_start: 0.7966 (tttp) cc_final: 0.7636 (tttp) REVERT: A 243 ARG cc_start: 0.7708 (ttt180) cc_final: 0.7400 (ttt180) REVERT: A 251 GLU cc_start: 0.6987 (pt0) cc_final: 0.6726 (pt0) REVERT: A 273 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6607 (pp20) REVERT: A 276 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6421 (mm-30) REVERT: A 327 GLU cc_start: 0.7295 (mp0) cc_final: 0.6505 (mp0) REVERT: A 328 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 346 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7062 (m-30) REVERT: A 369 ARG cc_start: 0.7902 (ttt90) cc_final: 0.7580 (ttp80) REVERT: A 379 ASP cc_start: 0.8405 (p0) cc_final: 0.7620 (p0) REVERT: A 383 ILE cc_start: 0.7739 (mt) cc_final: 0.7396 (mp) REVERT: A 386 MET cc_start: 0.7570 (ptm) cc_final: 0.7246 (ptt) REVERT: A 447 GLU cc_start: 0.7591 (tm-30) cc_final: 0.6860 (tm-30) REVERT: A 514 ARG cc_start: 0.7181 (tpp80) cc_final: 0.6741 (tpp80) REVERT: A 517 LYS cc_start: 0.7790 (ptmt) cc_final: 0.7556 (ptmt) REVERT: A 604 LYS cc_start: 0.8388 (mmmm) cc_final: 0.8120 (mmtp) REVERT: A 611 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7871 (pp) REVERT: A 613 ASP cc_start: 0.7385 (m-30) cc_final: 0.7101 (m-30) REVERT: A 632 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6570 (tp30) REVERT: A 649 LYS cc_start: 0.2181 (OUTLIER) cc_final: 0.1872 (pttm) REVERT: B 143 LEU cc_start: 0.7535 (tp) cc_final: 0.7240 (tp) REVERT: B 150 MET cc_start: 0.5980 (mmm) cc_final: 0.5480 (mmp) REVERT: B 160 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8198 (ttmt) REVERT: B 176 LEU cc_start: 0.8187 (tt) cc_final: 0.7966 (tt) REVERT: B 179 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6985 (tm-30) REVERT: B 221 THR cc_start: 0.6468 (p) cc_final: 0.6036 (p) REVERT: B 291 MET cc_start: 0.7082 (mtm) cc_final: 0.6449 (mtm) REVERT: B 295 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6981 (mt-10) REVERT: B 302 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6774 (mmt180) REVERT: B 324 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7006 (tm-30) REVERT: B 352 LYS cc_start: 0.7389 (tptt) cc_final: 0.7055 (tptt) REVERT: B 396 ILE cc_start: 0.8133 (tp) cc_final: 0.7867 (tp) REVERT: B 415 TYR cc_start: 0.7633 (m-80) cc_final: 0.7411 (m-80) REVERT: B 441 ASP cc_start: 0.7912 (t0) cc_final: 0.7577 (t70) REVERT: B 444 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7556 (tttt) REVERT: B 453 GLU cc_start: 0.6962 (mp0) cc_final: 0.6247 (mp0) REVERT: B 457 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7282 (ttmt) REVERT: B 494 MET cc_start: 0.7797 (tmm) cc_final: 0.7563 (tmm) REVERT: C 11 LYS cc_start: 0.7916 (tptp) cc_final: 0.7627 (tptp) REVERT: C 43 GLU cc_start: 0.7409 (mp0) cc_final: 0.7128 (mp0) REVERT: C 100 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7840 (mmmm) REVERT: C 118 LEU cc_start: 0.7782 (tp) cc_final: 0.6940 (tp) REVERT: C 119 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6510 (mm-30) REVERT: D 52 ASP cc_start: 0.7401 (t0) cc_final: 0.7144 (t0) REVERT: D 80 ASP cc_start: 0.6995 (m-30) cc_final: 0.6680 (m-30) REVERT: D 93 LYS cc_start: 0.8361 (mttp) cc_final: 0.8044 (mttt) REVERT: D 114 LEU cc_start: 0.7593 (mt) cc_final: 0.7262 (mt) REVERT: D 139 TYR cc_start: 0.7926 (m-80) cc_final: 0.7115 (m-80) REVERT: D 141 GLU cc_start: 0.7070 (pp20) cc_final: 0.6594 (pp20) REVERT: D 151 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7614 (mtpp) REVERT: D 194 MET cc_start: 0.6938 (mmm) cc_final: 0.6660 (mmm) REVERT: D 251 ILE cc_start: 0.8552 (mp) cc_final: 0.8331 (mt) REVERT: D 346 GLU cc_start: 0.7163 (tt0) cc_final: 0.6889 (mt-10) REVERT: D 389 GLU cc_start: 0.7134 (tp30) cc_final: 0.6770 (tp30) REVERT: D 405 ASN cc_start: 0.7865 (m-40) cc_final: 0.7598 (m-40) REVERT: D 414 GLU cc_start: 0.7198 (tt0) cc_final: 0.6863 (mt-10) REVERT: E 19 MET cc_start: 0.7322 (mmp) cc_final: 0.6970 (mmp) REVERT: E 84 ASP cc_start: 0.7591 (m-30) cc_final: 0.6989 (m-30) REVERT: F 7 THR cc_start: 0.8129 (m) cc_final: 0.7860 (t) REVERT: F 14 LYS cc_start: 0.7719 (mmmt) cc_final: 0.7390 (mmmt) REVERT: F 77 LYS cc_start: 0.7921 (ptpp) cc_final: 0.7470 (ptpp) REVERT: F 80 LYS cc_start: 0.8076 (tttm) cc_final: 0.7741 (tttt) REVERT: F 83 ASP cc_start: 0.7262 (t0) cc_final: 0.6851 (t0) REVERT: F 86 ARG cc_start: 0.7719 (ttt-90) cc_final: 0.7464 (ttt-90) REVERT: F 119 GLU cc_start: 0.7173 (mp0) cc_final: 0.6655 (mp0) REVERT: F 120 MET cc_start: 0.7915 (ttp) cc_final: 0.7665 (ttm) REVERT: F 133 GLU cc_start: 0.6851 (pp20) cc_final: 0.6388 (pp20) REVERT: F 138 ASP cc_start: 0.7859 (t0) cc_final: 0.7605 (t0) REVERT: F 142 MET cc_start: 0.7323 (ttt) cc_final: 0.7104 (ttp) REVERT: F 147 ARG cc_start: 0.7540 (mtt180) cc_final: 0.7338 (mtt180) REVERT: F 156 ARG cc_start: 0.7467 (mmt180) cc_final: 0.6500 (mtt180) REVERT: F 172 ARG cc_start: 0.7784 (ptm160) cc_final: 0.7198 (ttp80) REVERT: F 174 TRP cc_start: 0.7907 (t60) cc_final: 0.7672 (t60) REVERT: F 175 GLN cc_start: 0.7906 (mp10) cc_final: 0.7607 (mp10) REVERT: F 232 CYS cc_start: 0.6102 (OUTLIER) cc_final: 0.5812 (p) REVERT: F 237 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8366 (mtpt) REVERT: F 251 GLU cc_start: 0.7045 (pt0) cc_final: 0.6790 (pt0) REVERT: F 273 GLU cc_start: 0.7085 (pp20) cc_final: 0.6634 (pp20) REVERT: F 324 CYS cc_start: 0.7242 (m) cc_final: 0.6878 (m) REVERT: F 327 GLU cc_start: 0.7385 (mp0) cc_final: 0.7166 (mm-30) REVERT: F 328 GLU cc_start: 0.7890 (mt-10) cc_final: 0.6912 (mt-10) REVERT: F 348 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6083 (t80) REVERT: F 369 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7468 (ttp80) REVERT: F 379 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7553 (p0) REVERT: F 383 ILE cc_start: 0.7983 (mt) cc_final: 0.7617 (mp) REVERT: F 447 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6785 (tt0) REVERT: F 517 LYS cc_start: 0.7575 (ptmt) cc_final: 0.7357 (pttt) REVERT: F 570 ARG cc_start: 0.7900 (mmp80) cc_final: 0.7347 (mmp80) REVERT: F 577 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7621 (t) REVERT: F 583 GLU cc_start: 0.6293 (mp0) cc_final: 0.6081 (mp0) REVERT: F 586 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7110 (tp30) REVERT: F 611 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7820 (pp) REVERT: F 640 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7995 (p) REVERT: F 660 LYS cc_start: 0.6572 (ttpp) cc_final: 0.6342 (ttpp) REVERT: F 667 GLU cc_start: 0.7310 (mp0) cc_final: 0.7083 (mp0) REVERT: G 160 LYS cc_start: 0.8318 (ttmt) cc_final: 0.8076 (ttmt) REVERT: G 177 LYS cc_start: 0.8611 (tttm) cc_final: 0.8268 (tttm) REVERT: G 179 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6973 (tm-30) REVERT: G 189 LYS cc_start: 0.8372 (mttp) cc_final: 0.7929 (mttp) REVERT: G 191 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7797 (t) REVERT: G 206 ARG cc_start: 0.7082 (ttm170) cc_final: 0.6863 (ttm170) REVERT: G 246 ARG cc_start: 0.7765 (mmt90) cc_final: 0.7561 (mmt90) REVERT: G 291 MET cc_start: 0.7194 (mtm) cc_final: 0.6709 (mtm) REVERT: G 295 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6997 (mt-10) REVERT: G 324 GLU cc_start: 0.7504 (tm-30) cc_final: 0.6971 (tm-30) REVERT: G 352 LYS cc_start: 0.7334 (tptt) cc_final: 0.6856 (tptt) REVERT: G 385 ILE cc_start: 0.8391 (mm) cc_final: 0.8097 (mm) REVERT: G 396 ILE cc_start: 0.8177 (tp) cc_final: 0.7891 (tp) REVERT: G 444 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7488 (tmtt) REVERT: G 453 GLU cc_start: 0.6878 (mp0) cc_final: 0.6041 (mp0) REVERT: G 462 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7891 (ttm170) REVERT: G 466 LYS cc_start: 0.7878 (tptm) cc_final: 0.7539 (tptm) REVERT: G 485 LEU cc_start: 0.8306 (tp) cc_final: 0.8025 (tt) REVERT: G 487 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8118 (mtmm) REVERT: G 489 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7092 (tm-30) REVERT: G 494 MET cc_start: 0.7847 (tmm) cc_final: 0.7620 (tmm) REVERT: H 11 LYS cc_start: 0.8134 (tptp) cc_final: 0.7863 (tptp) REVERT: H 36 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6790 (tm-30) REVERT: H 43 GLU cc_start: 0.7306 (mp0) cc_final: 0.6921 (mp0) REVERT: H 119 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6242 (mm-30) REVERT: H 133 MET cc_start: 0.7490 (tmm) cc_final: 0.7171 (tmm) REVERT: I 13 THR cc_start: 0.8511 (p) cc_final: 0.8192 (p) REVERT: I 18 HIS cc_start: 0.8367 (m170) cc_final: 0.8081 (m90) REVERT: I 80 ASP cc_start: 0.7011 (m-30) cc_final: 0.6700 (m-30) REVERT: I 128 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7587 (mmmt) REVERT: I 139 TYR cc_start: 0.7952 (m-80) cc_final: 0.7145 (m-80) REVERT: I 145 LYS cc_start: 0.8169 (mttt) cc_final: 0.7890 (mttp) REVERT: I 151 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7330 (tttp) REVERT: I 202 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8168 (mm) REVERT: I 211 GLU cc_start: 0.7164 (tp30) cc_final: 0.6842 (tp30) REVERT: I 346 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: I 389 GLU cc_start: 0.7155 (tp30) cc_final: 0.6866 (tp30) REVERT: I 405 ASN cc_start: 0.7819 (m-40) cc_final: 0.7415 (m-40) REVERT: I 414 GLU cc_start: 0.7265 (tt0) cc_final: 0.7043 (mt-10) REVERT: J 34 ASN cc_start: 0.8341 (m-40) cc_final: 0.8078 (m110) REVERT: J 75 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7803 (mtm-85) REVERT: J 84 ASP cc_start: 0.7534 (m-30) cc_final: 0.6964 (m-30) REVERT: J 106 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6207 (mp0) outliers start: 148 outliers final: 104 residues processed: 1068 average time/residue: 0.4836 time to fit residues: 780.2393 Evaluate side-chains 1108 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 984 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 577 SER Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 621 TRP Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 640 THR Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 193 CYS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 372 ILE Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 525 HIS Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 346 GLU Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain I residue 364 LYS Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 392 VAL Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 1.9990 chunk 349 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 165 optimal weight: 0.0070 chunk 242 optimal weight: 0.7980 chunk 366 optimal weight: 0.5980 chunk 337 optimal weight: 0.5980 chunk 291 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 chunk 179 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 112 GLN B 115 GLN D 397 ASN E 34 ASN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** I 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29856 Z= 0.202 Angle : 0.679 11.683 40460 Z= 0.338 Chirality : 0.045 0.252 4532 Planarity : 0.005 0.083 5202 Dihedral : 6.092 59.199 4120 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.99 % Allowed : 26.68 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % 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: -1.91 (0.14), residues: 3712 helix: 0.06 (0.14), residues: 1480 sheet: -2.23 (0.26), residues: 388 loop : -2.21 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 339 HIS 0.005 0.001 HIS F 165 PHE 0.028 0.001 PHE A 572 TYR 0.020 0.001 TYR A 400 ARG 0.010 0.000 ARG A 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 976 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8377 (tttt) REVERT: A 14 LYS cc_start: 0.7658 (mmmt) cc_final: 0.7416 (mmmt) REVERT: A 61 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8526 (pt) REVERT: A 80 LYS cc_start: 0.8098 (tttm) cc_final: 0.7777 (tttt) REVERT: A 83 ASP cc_start: 0.7319 (t0) cc_final: 0.6938 (t0) REVERT: A 86 ARG cc_start: 0.7821 (ttt-90) cc_final: 0.7592 (ttt-90) REVERT: A 120 MET cc_start: 0.8009 (ttp) cc_final: 0.7779 (ttm) REVERT: A 138 ASP cc_start: 0.7758 (t0) cc_final: 0.7526 (t0) REVERT: A 142 MET cc_start: 0.7512 (ttt) cc_final: 0.7224 (ttp) REVERT: A 156 ARG cc_start: 0.7482 (mmt180) cc_final: 0.6439 (mtt180) REVERT: A 184 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7897 (mttm) REVERT: A 204 THR cc_start: 0.7026 (p) cc_final: 0.6809 (p) REVERT: A 232 CYS cc_start: 0.5430 (OUTLIER) cc_final: 0.5034 (p) REVERT: A 239 LYS cc_start: 0.7973 (tttp) cc_final: 0.7655 (tttp) REVERT: A 243 ARG cc_start: 0.7726 (ttt180) cc_final: 0.7430 (ttt180) REVERT: A 251 GLU cc_start: 0.6966 (pt0) cc_final: 0.6718 (pt0) REVERT: A 273 GLU cc_start: 0.7100 (pp20) cc_final: 0.6620 (pp20) REVERT: A 276 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6415 (mm-30) REVERT: A 327 GLU cc_start: 0.7294 (mp0) cc_final: 0.6494 (mp0) REVERT: A 328 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7204 (mt-10) REVERT: A 369 ARG cc_start: 0.7880 (ttt90) cc_final: 0.7591 (ttp80) REVERT: A 379 ASP cc_start: 0.8348 (p0) cc_final: 0.7590 (p0) REVERT: A 386 MET cc_start: 0.7568 (ptm) cc_final: 0.7332 (ptt) REVERT: A 447 GLU cc_start: 0.7645 (tm-30) cc_final: 0.6849 (tt0) REVERT: A 514 ARG cc_start: 0.7167 (tpp80) cc_final: 0.6767 (tpp80) REVERT: A 517 LYS cc_start: 0.7772 (ptmt) cc_final: 0.7559 (ptmt) REVERT: A 604 LYS cc_start: 0.8313 (mmmm) cc_final: 0.8050 (mmtp) REVERT: A 611 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7862 (pp) REVERT: A 613 ASP cc_start: 0.7377 (m-30) cc_final: 0.7102 (m-30) REVERT: A 632 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6502 (tp30) REVERT: A 649 LYS cc_start: 0.2025 (OUTLIER) cc_final: 0.1753 (pttm) REVERT: B 143 LEU cc_start: 0.7558 (tp) cc_final: 0.7252 (tp) REVERT: B 160 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8190 (ttmt) REVERT: B 176 LEU cc_start: 0.8183 (tt) cc_final: 0.7955 (tt) REVERT: B 179 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6955 (tm-30) REVERT: B 221 THR cc_start: 0.6494 (p) cc_final: 0.6064 (p) REVERT: B 274 HIS cc_start: 0.8458 (m90) cc_final: 0.8242 (m-70) REVERT: B 291 MET cc_start: 0.7063 (mtm) cc_final: 0.6398 (mtm) REVERT: B 295 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6989 (mt-10) REVERT: B 324 GLU cc_start: 0.7509 (tm-30) cc_final: 0.6978 (tm-30) REVERT: B 352 LYS cc_start: 0.7357 (tptt) cc_final: 0.7068 (tptt) REVERT: B 396 ILE cc_start: 0.8141 (tp) cc_final: 0.7877 (tp) REVERT: B 415 TYR cc_start: 0.7608 (m-80) cc_final: 0.7388 (m-80) REVERT: B 441 ASP cc_start: 0.7896 (t0) cc_final: 0.7567 (t70) REVERT: B 444 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7558 (tttt) REVERT: B 453 GLU cc_start: 0.6930 (mp0) cc_final: 0.6266 (mp0) REVERT: B 494 MET cc_start: 0.7793 (tmm) cc_final: 0.7557 (tmm) REVERT: C 11 LYS cc_start: 0.7941 (tptp) cc_final: 0.7670 (tptp) REVERT: C 43 GLU cc_start: 0.7411 (mp0) cc_final: 0.7134 (mp0) REVERT: C 48 ILE cc_start: 0.8665 (mt) cc_final: 0.8361 (mp) REVERT: C 100 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7888 (mmmm) REVERT: C 118 LEU cc_start: 0.7768 (tp) cc_final: 0.6973 (tp) REVERT: C 119 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6491 (mm-30) REVERT: D 14 ARG cc_start: 0.8368 (mtm110) cc_final: 0.8072 (mtm180) REVERT: D 52 ASP cc_start: 0.7409 (t0) cc_final: 0.7148 (t0) REVERT: D 80 ASP cc_start: 0.6981 (m-30) cc_final: 0.6650 (m-30) REVERT: D 100 MET cc_start: 0.7354 (mmm) cc_final: 0.6829 (mmm) REVERT: D 114 LEU cc_start: 0.7616 (mt) cc_final: 0.7291 (mt) REVERT: D 128 LYS cc_start: 0.7869 (mmmt) cc_final: 0.7632 (mmmt) REVERT: D 139 TYR cc_start: 0.7889 (m-80) cc_final: 0.7086 (m-80) REVERT: D 141 GLU cc_start: 0.7053 (pp20) cc_final: 0.6579 (pp20) REVERT: D 151 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7624 (mtpp) REVERT: D 194 MET cc_start: 0.6951 (mmm) cc_final: 0.6686 (mmm) REVERT: D 251 ILE cc_start: 0.8558 (mp) cc_final: 0.8334 (mt) REVERT: D 346 GLU cc_start: 0.7145 (tt0) cc_final: 0.6871 (mt-10) REVERT: D 361 VAL cc_start: 0.8487 (t) cc_final: 0.8225 (m) REVERT: D 389 GLU cc_start: 0.7107 (tp30) cc_final: 0.6732 (tp30) REVERT: D 414 GLU cc_start: 0.7215 (tt0) cc_final: 0.6839 (mt-10) REVERT: E 19 MET cc_start: 0.7314 (mmp) cc_final: 0.6987 (mmp) REVERT: E 84 ASP cc_start: 0.7545 (m-30) cc_final: 0.6963 (m-30) REVERT: F 7 THR cc_start: 0.8100 (m) cc_final: 0.7842 (t) REVERT: F 77 LYS cc_start: 0.7939 (ptpp) cc_final: 0.7717 (ptpp) REVERT: F 80 LYS cc_start: 0.8050 (tttm) cc_final: 0.7715 (tttt) REVERT: F 83 ASP cc_start: 0.7250 (t0) cc_final: 0.6889 (t0) REVERT: F 86 ARG cc_start: 0.7724 (ttt-90) cc_final: 0.7472 (ttt-90) REVERT: F 119 GLU cc_start: 0.7157 (mp0) cc_final: 0.6662 (mp0) REVERT: F 120 MET cc_start: 0.7928 (ttp) cc_final: 0.7642 (ttm) REVERT: F 133 GLU cc_start: 0.6858 (pp20) cc_final: 0.6395 (pp20) REVERT: F 142 MET cc_start: 0.7363 (ttt) cc_final: 0.7088 (ttp) REVERT: F 146 ASN cc_start: 0.7591 (p0) cc_final: 0.7133 (p0) REVERT: F 156 ARG cc_start: 0.7451 (mmt180) cc_final: 0.6881 (mtt90) REVERT: F 172 ARG cc_start: 0.7780 (ptm160) cc_final: 0.7184 (ttp80) REVERT: F 174 TRP cc_start: 0.7874 (t60) cc_final: 0.7547 (t60) REVERT: F 175 GLN cc_start: 0.7895 (mp10) cc_final: 0.7590 (mp10) REVERT: F 232 CYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5820 (p) REVERT: F 237 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8381 (mtpt) REVERT: F 251 GLU cc_start: 0.7034 (pt0) cc_final: 0.6789 (pt0) REVERT: F 273 GLU cc_start: 0.7086 (pp20) cc_final: 0.6655 (pp20) REVERT: F 324 CYS cc_start: 0.7256 (m) cc_final: 0.6908 (m) REVERT: F 327 GLU cc_start: 0.7373 (mp0) cc_final: 0.7071 (mp0) REVERT: F 328 GLU cc_start: 0.7866 (mt-10) cc_final: 0.6893 (mt-10) REVERT: F 348 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6097 (t80) REVERT: F 369 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7491 (ttp80) REVERT: F 379 ASP cc_start: 0.8291 (p0) cc_final: 0.7492 (p0) REVERT: F 383 ILE cc_start: 0.7980 (mt) cc_final: 0.7621 (mp) REVERT: F 386 MET cc_start: 0.7482 (ptp) cc_final: 0.7269 (ptm) REVERT: F 447 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6651 (tt0) REVERT: F 517 LYS cc_start: 0.7559 (ptmt) cc_final: 0.7350 (pttt) REVERT: F 570 ARG cc_start: 0.7848 (mmp80) cc_final: 0.7339 (mmp80) REVERT: F 577 SER cc_start: 0.7904 (OUTLIER) cc_final: 0.7589 (t) REVERT: F 586 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: F 611 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7825 (pp) REVERT: F 640 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7980 (p) REVERT: F 660 LYS cc_start: 0.6487 (ttpp) cc_final: 0.6255 (ttpp) REVERT: F 667 GLU cc_start: 0.7290 (mp0) cc_final: 0.7064 (mp0) REVERT: G 160 LYS cc_start: 0.8306 (ttmt) cc_final: 0.8049 (ttmt) REVERT: G 177 LYS cc_start: 0.8566 (tttm) cc_final: 0.8250 (tttm) REVERT: G 179 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6936 (tm-30) REVERT: G 189 LYS cc_start: 0.8350 (mttp) cc_final: 0.7907 (mttp) REVERT: G 191 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7804 (t) REVERT: G 295 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6969 (mt-10) REVERT: G 352 LYS cc_start: 0.7289 (tptt) cc_final: 0.6843 (tptt) REVERT: G 396 ILE cc_start: 0.8174 (tp) cc_final: 0.7715 (tp) REVERT: G 441 ASP cc_start: 0.7836 (t0) cc_final: 0.7376 (t0) REVERT: G 444 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7493 (tmtt) REVERT: G 453 GLU cc_start: 0.6867 (mp0) cc_final: 0.6044 (mp0) REVERT: G 462 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7902 (ttm170) REVERT: G 466 LYS cc_start: 0.7825 (tptm) cc_final: 0.7502 (mmmm) REVERT: G 485 LEU cc_start: 0.8299 (tp) cc_final: 0.8048 (tt) REVERT: G 487 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8114 (mtmm) REVERT: G 489 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7084 (tm-30) REVERT: G 494 MET cc_start: 0.7851 (tmm) cc_final: 0.7632 (tmm) REVERT: H 11 LYS cc_start: 0.8126 (tptp) cc_final: 0.7847 (tptp) REVERT: H 35 ARG cc_start: 0.6674 (mtm-85) cc_final: 0.6083 (mtm-85) REVERT: H 36 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6779 (tm-30) REVERT: H 119 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6202 (mm-30) REVERT: H 133 MET cc_start: 0.7471 (tmm) cc_final: 0.7198 (tmm) REVERT: I 13 THR cc_start: 0.8510 (p) cc_final: 0.7964 (p) REVERT: I 18 HIS cc_start: 0.8346 (m170) cc_final: 0.7990 (m90) REVERT: I 80 ASP cc_start: 0.7009 (m-30) cc_final: 0.6704 (m-30) REVERT: I 128 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7570 (mmmt) REVERT: I 139 TYR cc_start: 0.7938 (m-80) cc_final: 0.7178 (m-80) REVERT: I 145 LYS cc_start: 0.8121 (mttt) cc_final: 0.7844 (mttp) REVERT: I 151 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7251 (tttp) REVERT: I 211 GLU cc_start: 0.7133 (tp30) cc_final: 0.6818 (tp30) REVERT: I 311 GLU cc_start: 0.6353 (tt0) cc_final: 0.6118 (tt0) REVERT: I 346 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: I 389 GLU cc_start: 0.7142 (tp30) cc_final: 0.6864 (tp30) REVERT: I 414 GLU cc_start: 0.7251 (tt0) cc_final: 0.7036 (mt-10) REVERT: J 19 MET cc_start: 0.7660 (mmm) cc_final: 0.7212 (mmp) REVERT: J 44 ASP cc_start: 0.7193 (m-30) cc_final: 0.6724 (m-30) REVERT: J 84 ASP cc_start: 0.7521 (m-30) cc_final: 0.6966 (m-30) REVERT: J 106 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6154 (mp0) outliers start: 125 outliers final: 88 residues processed: 1037 average time/residue: 0.4799 time to fit residues: 748.8402 Evaluate side-chains 1065 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 961 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 575 VAL Chi-restraints excluded: chain F residue 577 SER Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 621 TRP Chi-restraints excluded: chain F residue 628 PHE Chi-restraints excluded: chain F residue 640 THR Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 193 CYS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 372 ILE Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 525 HIS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 346 GLU Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain I residue 364 LYS Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 269 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 300 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN D 397 ASN D 405 ASN E 34 ASN E 116 ASN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** I 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN J 116 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.119340 restraints weight = 40799.709| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.09 r_work: 0.3348 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29856 Z= 0.322 Angle : 0.716 11.715 40460 Z= 0.358 Chirality : 0.049 0.273 4532 Planarity : 0.005 0.078 5202 Dihedral : 6.178 59.686 4115 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 4.15 % Allowed : 26.74 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.97 (0.13), residues: 3712 helix: -0.03 (0.14), residues: 1480 sheet: -2.45 (0.25), residues: 392 loop : -2.15 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 621 HIS 0.006 0.001 HIS F 165 PHE 0.030 0.002 PHE A 572 TYR 0.019 0.002 TYR D 330 ARG 0.007 0.000 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11597.66 seconds wall clock time: 206 minutes 54.42 seconds (12414.42 seconds total)