Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 04:47:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/04_2023/7t2r_25633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/04_2023/7t2r_25633.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/04_2023/7t2r_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_25633/04_2023/7t2r_25633_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/04_2023/7t2r_25633_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/04_2023/7t2r_25633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/04_2023/7t2r_25633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/04_2023/7t2r_25633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2r_25633/04_2023/7t2r_25633_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 14.96, per 1000 atoms: 0.51 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: 11.21 Conformation dependent library (CDL) restraints added in 4.1 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: 2.80 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: 8.29 Time building geometry restraints manager: 12.09 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.280 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 73.230 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.620 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 3.447 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 outliers start: 164 outliers final: 62 residues processed: 1252 average time/residue: 0.4670 time to fit residues: 882.0254 Evaluate side-chains 1085 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1023 time to evaluate : 3.245 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.2694 time to fit residues: 35.9124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 chunk 95 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 149 optimal weight: 0.0020 chunk 288 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 334 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN A 97 ASN 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 405 ASN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN E 62 ASN F 26 ASN F 38 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 145 HIS F 344 HIS F 366 GLN F 391 GLN F 407 HIS F 409 ASN ** F 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 HIS G 505 GLN H 88 HIS I 166 HIS I 267 HIS I 331 HIS I 386 GLN I 405 ASN J 34 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 29856 Z= 0.214 Angle : 0.688 9.601 40460 Z= 0.350 Chirality : 0.046 0.203 4532 Planarity : 0.006 0.071 5202 Dihedral : 5.577 38.142 4082 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer Outliers : 3.96 % 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: -3.43 (0.12), residues: 3712 helix: -1.42 (0.12), residues: 1486 sheet: -2.90 (0.23), residues: 390 loop : -2.89 (0.13), residues: 1836 *********************** 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 1188 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1064 time to evaluate : 3.644 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 outliers start: 124 outliers final: 56 residues processed: 1129 average time/residue: 0.4824 time to fit residues: 817.6305 Evaluate side-chains 1060 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1004 time to evaluate : 3.266 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.2912 time to fit residues: 33.8151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 227 optimal weight: 0.0770 chunk 92 optimal weight: 0.3980 chunk 334 optimal weight: 0.2980 chunk 361 optimal weight: 0.6980 chunk 298 optimal weight: 0.7980 chunk 331 optimal weight: 0.6980 chunk 114 optimal weight: 0.3980 chunk 268 optimal weight: 8.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 53 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 ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS H 149 GLN I 405 ASN J 34 ASN J 62 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 29856 Z= 0.190 Angle : 0.665 8.714 40460 Z= 0.332 Chirality : 0.045 0.202 4532 Planarity : 0.005 0.055 5202 Dihedral : 5.390 41.527 4082 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer Outliers : 3.29 % 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: -2.83 (0.13), residues: 3712 helix: -0.83 (0.13), residues: 1480 sheet: -2.61 (0.25), residues: 364 loop : -2.65 (0.13), residues: 1868 *********************** 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 1154 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1051 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 outliers start: 103 outliers final: 40 residues processed: 1094 average time/residue: 0.4839 time to fit residues: 794.2123 Evaluate side-chains 1042 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1002 time to evaluate : 3.356 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3014 time to fit residues: 26.3287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 330 optimal weight: 5.9990 chunk 251 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 159 optimal weight: 0.1980 chunk 224 optimal weight: 1.9990 chunk 335 optimal weight: 0.8980 chunk 355 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 38 GLN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN A 97 ASN A 338 ASN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN E 34 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** I 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 ASN J 34 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2532 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= 0.218 Angle : 0.667 12.447 40460 Z= 0.333 Chirality : 0.046 0.348 4532 Planarity : 0.005 0.051 5202 Dihedral : 5.275 39.742 4082 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer Outliers : 3.38 % 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: -2.54 (0.13), residues: 3712 helix: -0.56 (0.13), residues: 1468 sheet: -2.54 (0.25), residues: 368 loop : -2.47 (0.13), residues: 1876 *********************** 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 1118 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1012 time to evaluate : 3.199 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 outliers start: 106 outliers final: 44 residues processed: 1065 average time/residue: 0.4876 time to fit residues: 780.7886 Evaluate side-chains 1033 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 989 time to evaluate : 3.269 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3151 time to fit residues: 28.7744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 264 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 303 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 181 optimal weight: 0.0470 chunk 319 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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** D 40 GLN D 397 ASN ** D 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN E 34 ASN E 62 ASN E 116 ASN F 87 GLN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** G 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN ** I 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN J 116 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 29856 Z= 0.207 Angle : 0.666 9.000 40460 Z= 0.332 Chirality : 0.045 0.239 4532 Planarity : 0.005 0.051 5202 Dihedral : 5.194 41.135 4082 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer Outliers : 3.06 % 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: -2.30 (0.13), residues: 3712 helix: -0.33 (0.13), residues: 1474 sheet: -2.40 (0.25), residues: 368 loop : -2.38 (0.13), residues: 1870 *********************** 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 1104 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1008 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 48 residues processed: 1048 average time/residue: 0.5096 time to fit residues: 803.1177 Evaluate side-chains 1035 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 987 time to evaluate : 3.478 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.3285 time to fit residues: 33.3801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 6.9990 chunk 320 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 356 optimal weight: 4.9990 chunk 295 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 117 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- 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 112 GLN D 37 HIS D 397 ASN E 34 ASN E 116 ASN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS I 30 HIS I 405 ASN J 34 ASN J 116 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 29856 Z= 0.296 Angle : 0.704 11.206 40460 Z= 0.352 Chirality : 0.048 0.336 4532 Planarity : 0.005 0.054 5202 Dihedral : 5.356 42.460 4082 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer Outliers : 2.65 % 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: -2.29 (0.13), residues: 3712 helix: -0.35 (0.13), residues: 1482 sheet: -2.46 (0.25), residues: 372 loop : -2.32 (0.13), residues: 1858 *********************** 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 1103 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1020 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 42 residues processed: 1053 average time/residue: 0.5130 time to fit residues: 812.5427 Evaluate side-chains 1034 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 992 time to evaluate : 3.306 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.3087 time to fit residues: 28.1246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 260 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 354 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 610 ASN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN D 397 ASN E 34 ASN E 116 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS G 509 ASN ** G 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 ASN J 34 ASN J 116 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 29856 Z= 0.327 Angle : 0.735 11.222 40460 Z= 0.365 Chirality : 0.050 0.357 4532 Planarity : 0.005 0.072 5202 Dihedral : 5.518 45.986 4082 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.62 % Favored : 90.36 % Rotamer Outliers : 2.55 % 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: -2.30 (0.13), residues: 3712 helix: -0.38 (0.13), residues: 1496 sheet: -2.50 (0.25), residues: 372 loop : -2.32 (0.13), residues: 1844 *********************** 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 1105 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1025 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 42 residues processed: 1055 average time/residue: 0.5056 time to fit residues: 799.4972 Evaluate side-chains 1049 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1007 time to evaluate : 3.724 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2959 time to fit residues: 27.8244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 211 optimal weight: 0.3980 chunk 106 optimal weight: 0.0170 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 241 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 278 optimal weight: 0.2980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN D 397 ASN E 34 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** G 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29856 Z= 0.233 Angle : 0.718 13.683 40460 Z= 0.356 Chirality : 0.047 0.287 4532 Planarity : 0.005 0.053 5202 Dihedral : 5.347 40.290 4082 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer Outliers : 1.34 % 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: -2.18 (0.13), residues: 3712 helix: -0.25 (0.14), residues: 1486 sheet: -2.34 (0.26), residues: 368 loop : -2.30 (0.13), residues: 1858 *********************** 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 1045 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1003 time to evaluate : 3.208 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 outliers start: 42 outliers final: 24 residues processed: 1018 average time/residue: 0.5069 time to fit residues: 775.0827 Evaluate side-chains 1003 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 979 time to evaluate : 3.436 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3190 time to fit residues: 18.5839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 0.9990 chunk 339 optimal weight: 0.0770 chunk 310 optimal weight: 0.6980 chunk 330 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 298 optimal weight: 0.0770 chunk 312 optimal weight: 1.9990 chunk 329 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 262 GLN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN E 34 ASN E 116 ASN ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** G 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 ASN ** J 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 29856 Z= 0.224 Angle : 0.738 13.310 40460 Z= 0.365 Chirality : 0.046 0.313 4532 Planarity : 0.005 0.093 5202 Dihedral : 5.427 59.317 4082 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer Outliers : 1.18 % 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: -2.10 (0.13), residues: 3712 helix: -0.19 (0.14), residues: 1498 sheet: -2.13 (0.26), residues: 386 loop : -2.30 (0.14), residues: 1828 *********************** 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 1028 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 991 time to evaluate : 3.108 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 outliers start: 37 outliers final: 15 residues processed: 1011 average time/residue: 0.4946 time to fit residues: 750.0404 Evaluate side-chains 984 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 969 time to evaluate : 3.223 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3042 time to fit residues: 13.0857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 242 optimal weight: 0.6980 chunk 366 optimal weight: 0.7980 chunk 337 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 386 GLN D 397 ASN E 34 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** G 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS J 34 ASN J 116 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 29856 Z= 0.336 Angle : 0.796 14.704 40460 Z= 0.394 Chirality : 0.050 0.386 4532 Planarity : 0.006 0.072 5202 Dihedral : 5.523 43.162 4082 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer Outliers : 0.54 % 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: -2.14 (0.13), residues: 3712 helix: -0.24 (0.14), residues: 1470 sheet: -2.29 (0.26), residues: 368 loop : -2.25 (0.13), residues: 1874 ********************** 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 1015 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 998 time to evaluate : 3.290 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 outliers start: 17 outliers final: 9 residues processed: 1005 average time/residue: 0.5461 time to fit residues: 830.7419 Evaluate side-chains 990 residues out of total 3134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 981 time to evaluate : 3.490 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4203 time to fit residues: 11.6291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 292 optimal weight: 0.0040 chunk 122 optimal weight: 1.9990 chunk 300 optimal weight: 4.9990 chunk 37 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 overall best weight: 0.7672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN E 34 ASN E 116 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 GLN ** G 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS J 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122381 restraints weight = 40901.201| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.08 r_work: 0.3386 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 29856 Z= 0.255 Angle : 0.770 14.299 40460 Z= 0.380 Chirality : 0.048 0.327 4532 Planarity : 0.005 0.054 5202 Dihedral : 5.448 42.030 4082 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer Outliers : 0.96 % 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: -2.07 (0.13), residues: 3712 helix: -0.16 (0.14), residues: 1466 sheet: -2.25 (0.26), residues: 368 loop : -2.23 (0.13), residues: 1878 =============================================================================== Job complete usr+sys time: 11471.38 seconds wall clock time: 205 minutes 11.16 seconds (12311.16 seconds total)