Starting phenix.real_space_refine on Sun Feb 18 12:08:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0h_15781/02_2024/8b0h_15781.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0h_15781/02_2024/8b0h_15781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0h_15781/02_2024/8b0h_15781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0h_15781/02_2024/8b0h_15781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0h_15781/02_2024/8b0h_15781.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0h_15781/02_2024/8b0h_15781.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 611 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 268 5.16 5 C 23276 2.51 5 N 6409 2.21 5 O 7162 1.98 5 H 35735 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F ASP 172": "OD1" <-> "OD2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E ASP 192": "OD1" <-> "OD2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "E GLU 430": "OE1" <-> "OE2" Residue "E ASP 458": "OD1" <-> "OD2" Residue "E PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 798": "OE1" <-> "OE2" Residue "A GLU 826": "OE1" <-> "OE2" Residue "A TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A TYR 961": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1165": "OD1" <-> "OD2" Residue "A GLU 1177": "OE1" <-> "OE2" Residue "A TYR 1193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1199": "OD1" <-> "OD2" Residue "A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1289": "OD1" <-> "OD2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C ASP 320": "OD1" <-> "OD2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C GLU 548": "OE1" <-> "OE2" Residue "C GLU 557": "OE1" <-> "OE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B ASP 492": "OD1" <-> "OD2" Residue "B TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 689": "OD1" <-> "OD2" Residue "H ASP 59": "OD1" <-> "OD2" Residue "H ASP 63": "OD1" <-> "OD2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H GLU 128": "OE1" <-> "OE2" Residue "H ASP 163": "OD1" <-> "OD2" Residue "H ASP 165": "OD1" <-> "OD2" Residue "H GLU 270": "OE1" <-> "OE2" Residue "H ASP 301": "OD1" <-> "OD2" Residue "H TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 336": "OE1" <-> "OE2" Residue "H GLU 418": "OE1" <-> "OE2" Residue "H ASP 502": "OD1" <-> "OD2" Residue "I PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 75": "OD1" <-> "OD2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 291": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72850 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1209 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "D" Number of atoms: 7926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7926 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 483} Chain breaks: 2 Chain: "F" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2602 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain: "E" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 7866 Classifications: {'peptide': 513} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 497} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 19678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 19678 Classifications: {'peptide': 1245} Link IDs: {'PCIS': 2, 'PTRANS': 56, 'TRANS': 1186} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 9762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 9762 Classifications: {'peptide': 646} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 609} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 11267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 11267 Classifications: {'peptide': 737} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 699} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 6310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6310 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 15, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 6230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6230 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N MET G 0 " occ=0.64 ... (15 atoms not shown) pdb=" HE3 MET G 0 " occ=0.64 residue: pdb=" N GLN G 2 " occ=0.71 ... (15 atoms not shown) pdb="HE22 GLN G 2 " occ=0.71 residue: pdb=" N PHE G 23 " occ=0.61 ... (18 atoms not shown) pdb=" HZ PHE G 23 " occ=0.61 residue: pdb=" N THR G 52 " occ=0.43 ... (12 atoms not shown) pdb="HG23 THR G 52 " occ=0.43 Time building chain proxies: 24.93, per 1000 atoms: 0.34 Number of scatterers: 72850 At special positions: 0 Unit cell: (128.805, 191.13, 259.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 268 16.00 O 7162 8.00 N 6409 7.00 C 23276 6.00 H 35735 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=97, symmetry=0 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 26 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 13 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 45 " - pdb=" SG CYS G 63 " distance=2.02 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 69 " distance=2.02 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 46 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 56 " distance=2.02 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 62 " distance=2.04 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 79 " distance=2.03 Simple disulfide: pdb=" SG CYS D 73 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 146 " distance=2.03 Simple disulfide: pdb=" SG CYS D 324 " - pdb=" SG CYS D 349 " distance=2.03 Simple disulfide: pdb=" SG CYS D 449 " - pdb=" SG CYS D 496 " distance=2.03 Simple disulfide: pdb=" SG CYS D 451 " - pdb=" SG CYS D 467 " distance=2.03 Simple disulfide: pdb=" SG CYS D 454 " - pdb=" SG CYS D 469 " distance=2.03 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS D 480 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 44 " distance=2.03 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 54 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 78 " distance=2.03 Simple disulfide: pdb=" SG CYS E 72 " - pdb=" SG CYS E 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 85 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 345 " - pdb=" SG CYS E 369 " distance=2.04 Simple disulfide: pdb=" SG CYS E 467 " - pdb=" SG CYS E 514 " distance=2.03 Simple disulfide: pdb=" SG CYS E 469 " - pdb=" SG CYS E 485 " distance=2.03 Simple disulfide: pdb=" SG CYS E 472 " - pdb=" SG CYS E 487 " distance=2.03 Simple disulfide: pdb=" SG CYS E 489 " - pdb=" SG CYS E 498 " distance=2.03 Simple disulfide: pdb=" SG CYS E 521 " - pdb=" SG CYS E 554 " distance=2.03 Simple disulfide: pdb=" SG CYS E 532 " - pdb=" SG CYS E 544 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 810 " distance=2.03 Simple disulfide: pdb=" SG CYS A 634 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 856 " - pdb=" SG CYS A 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A1101 " - pdb=" SG CYS A1159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 39 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 79 " distance=2.03 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 103 " - pdb=" SG CYS C 119 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 337 " - pdb=" SG CYS C 353 " distance=2.04 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 560 " distance=2.03 Simple disulfide: pdb=" SG CYS C 455 " - pdb=" SG CYS C 505 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 460 " - pdb=" SG CYS C 475 " distance=2.04 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 545 " distance=2.03 Simple disulfide: pdb=" SG CYS C 523 " - pdb=" SG CYS C 535 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 613 " distance=2.03 Simple disulfide: pdb=" SG CYS C 599 " - pdb=" SG CYS C 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 73 " distance=2.03 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 78 " distance=2.04 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 127 " distance=2.02 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 158 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 420 " distance=2.04 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 623 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 539 " distance=2.03 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 552 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 589 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 686 " distance=2.03 Simple disulfide: pdb=" SG CYS B 672 " - pdb=" SG CYS B 699 " distance=2.03 Simple disulfide: pdb=" SG CYS B 704 " - pdb=" SG CYS B 746 " distance=2.04 Simple disulfide: pdb=" SG CYS B 732 " - pdb=" SG CYS B 761 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 57 " distance=2.03 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 67 " distance=2.04 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 73 " distance=2.03 Simple disulfide: pdb=" SG CYS H 80 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 86 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 113 " distance=2.03 Simple disulfide: pdb=" SG CYS H 121 " - pdb=" SG CYS H 160 " distance=2.04 Simple disulfide: pdb=" SG CYS H 489 " - pdb=" SG CYS H 505 " distance=2.03 Simple disulfide: pdb=" SG CYS H 492 " - pdb=" SG CYS H 507 " distance=2.03 Simple disulfide: pdb=" SG CYS H 509 " - pdb=" SG CYS H 518 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 57 " distance=2.03 Simple disulfide: pdb=" SG CYS I 33 " - pdb=" SG CYS I 67 " distance=2.03 Simple disulfide: pdb=" SG CYS I 36 " - pdb=" SG CYS I 73 " distance=2.04 Simple disulfide: pdb=" SG CYS I 80 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 86 " - pdb=" SG CYS I 104 " distance=2.04 Simple disulfide: pdb=" SG CYS I 98 " - pdb=" SG CYS I 113 " distance=2.03 Simple disulfide: pdb=" SG CYS I 121 " - pdb=" SG CYS I 160 " distance=2.03 Simple disulfide: pdb=" SG CYS I 489 " - pdb=" SG CYS I 505 " distance=2.03 Simple disulfide: pdb=" SG CYS I 509 " - pdb=" SG CYS I 518 " 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=0, symmetry=0 Time building additional restraints: 44.71 Conformation dependent library (CDL) restraints added in 6.2 seconds 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8730 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 68 sheets defined 20.1% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'G' and resid 46 through 55 Processing helix chain 'G' and resid 71 through 75 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 117 through 122 removed outlier: 3.665A pdb=" N LEU D 121 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 122 " --> pdb=" O ILE D 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 117 through 122' Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.928A pdb=" N TYR D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.753A pdb=" N GLN D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 427 through 447 removed outlier: 3.621A pdb=" N GLU D 440 " --> pdb=" O LYS D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 451 Processing helix chain 'F' and resid 23 through 28 Processing helix chain 'F' and resid 40 through 45 removed outlier: 4.079A pdb=" N GLN F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 152 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 172 through 176 removed outlier: 4.136A pdb=" N VAL F 176 " --> pdb=" O GLN F 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 119 through 123 removed outlier: 3.608A pdb=" N ALA E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 119 through 123' Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 281 through 291 Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 397 through 407 Processing helix chain 'E' and resid 409 through 423 removed outlier: 3.590A pdb=" N LYS E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR E 422 " --> pdb=" O ARG E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 441 removed outlier: 3.612A pdb=" N ARG E 439 " --> pdb=" O GLU E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 464 Processing helix chain 'E' and resid 465 through 469 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.914A pdb=" N LYS A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 607 through 613 removed outlier: 4.070A pdb=" N GLN A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 641 through 649 Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.769A pdb=" N GLN A 663 " --> pdb=" O ASP A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1001 Processing helix chain 'A' and resid 1009 through 1026 Proline residue: A1017 - end of helix removed outlier: 3.810A pdb=" N TYR A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1041 through 1059 removed outlier: 3.558A pdb=" N TYR A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1089 removed outlier: 3.674A pdb=" N GLN A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1096 through 1112 Processing helix chain 'A' and resid 1140 through 1157 removed outlier: 3.534A pdb=" N LEU A1144 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1180 Processing helix chain 'A' and resid 1184 through 1198 removed outlier: 3.541A pdb=" N LEU A1188 " --> pdb=" O SER A1184 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A1197 " --> pdb=" O TYR A1193 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A1198 " --> pdb=" O ALA A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1215 Processing helix chain 'A' and resid 1241 through 1261 Processing helix chain 'A' and resid 1263 through 1276 Proline residue: A1269 - end of helix Processing helix chain 'A' and resid 1286 through 1308 removed outlier: 3.550A pdb=" N THR A1290 " --> pdb=" O SER A1286 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A1305 " --> pdb=" O SER A1301 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 171 through 174 Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.572A pdb=" N HIS C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.710A pdb=" N TYR C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 390 Processing helix chain 'C' and resid 399 through 410 Processing helix chain 'C' and resid 425 through 428 Processing helix chain 'C' and resid 433 through 453 Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 547 through 557 removed outlier: 4.464A pdb=" N ARG C 554 " --> pdb=" O LEU C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 561 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 189 through 194 removed outlier: 3.969A pdb=" N MET B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 194' Processing helix chain 'B' and resid 335 through 345 Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.859A pdb=" N ILE B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE B 358 " --> pdb=" O TYR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.524A pdb=" N GLU B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 499 through 519 Processing helix chain 'B' and resid 520 through 523 Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 106 through 110 removed outlier: 4.122A pdb=" N ASP H 109 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 135 Processing helix chain 'H' and resid 295 through 305 Processing helix chain 'H' and resid 310 through 322 Processing helix chain 'H' and resid 412 through 425 removed outlier: 4.175A pdb=" N GLU H 418 " --> pdb=" O LYS H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 441 removed outlier: 3.609A pdb=" N PHE H 434 " --> pdb=" O ASP H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 459 Processing helix chain 'H' and resid 465 through 484 Processing helix chain 'H' and resid 485 through 489 Processing helix chain 'I' and resid 93 through 97 Processing helix chain 'I' and resid 107 through 113 Processing helix chain 'I' and resid 129 through 134 Processing helix chain 'I' and resid 295 through 304 Processing helix chain 'I' and resid 310 through 321 Processing helix chain 'I' and resid 342 through 350 removed outlier: 3.948A pdb=" N ARG I 348 " --> pdb=" O ALA I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 353 through 358 Processing helix chain 'I' and resid 412 through 424 removed outlier: 3.810A pdb=" N ALA I 416 " --> pdb=" O THR I 412 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 442 removed outlier: 3.899A pdb=" N ASN I 442 " --> pdb=" O ALA I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 459 Processing helix chain 'I' and resid 465 through 484 Processing helix chain 'I' and resid 485 through 489 Processing sheet with id=AA1, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'G' and resid 25 through 31 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 34 through 40 current: chain 'D' and resid 215 through 252 removed outlier: 5.301A pdb=" N SER D 216 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP D 328 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N SER D 218 " --> pdb=" O LYS D 326 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LYS D 326 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARG D 220 " --> pdb=" O CYS D 324 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N CYS D 324 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS D 222 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N HIS D 322 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR D 224 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN D 320 " --> pdb=" O TYR D 224 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ARG D 226 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU D 318 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR D 228 " --> pdb=" O TYR D 316 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR D 316 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ARG D 230 " --> pdb=" O GLY D 314 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY D 314 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER D 232 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLU D 312 " --> pdb=" O SER D 232 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N THR D 234 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA D 310 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N SER D 236 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LYS D 308 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N PHE D 238 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET D 306 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N HIS D 240 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU D 304 " --> pdb=" O HIS D 240 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ARG D 242 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TYR D 302 " --> pdb=" O ARG D 242 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP D 244 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N TYR D 300 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU D 246 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY D 298 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR D 292 " --> pdb=" O LEU D 252 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 345 through 374 current: chain 'E' and resid 240 through 273 removed outlier: 6.639A pdb=" N MET E 317 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N HIS E 270 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY E 315 " --> pdb=" O HIS E 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 370 through 395 current: chain 'C' and resid 151 through 154 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 151 through 154 current: chain 'C' and resid 226 through 263 removed outlier: 6.755A pdb=" N LEU C 309 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA C 260 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY C 307 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE C 262 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLN C 305 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 316 " --> pdb=" O GLU C 374 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 349 through 378 current: chain 'B' and resid 204 through 207 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 204 through 207 current: chain 'B' and resid 286 through 327 removed outlier: 5.187A pdb=" N SER B 287 " --> pdb=" O ARG B 407 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG B 407 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG B 289 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LYS B 405 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU B 291 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLU B 403 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE B 293 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG B 401 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N HIS B 295 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS B 399 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER B 297 " --> pdb=" O LYS B 397 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS B 397 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE B 299 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLU B 395 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLN B 301 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU B 393 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE B 303 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU B 391 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ALA B 305 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N SER B 389 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS B 307 " --> pdb=" O LYS B 387 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LYS B 387 " --> pdb=" O HIS B 307 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LYS B 309 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU B 385 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER B 311 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 383 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE B 313 " --> pdb=" O PHE B 381 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE B 381 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ARG B 315 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 379 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS B 317 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU B 377 " --> pdb=" O HIS B 317 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL B 319 " --> pdb=" O TYR B 375 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR B 375 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYS B 321 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY B 373 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR B 367 " --> pdb=" O THR B 327 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 413 through 445 current: chain 'H' and resid 145 through 147 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 145 through 147 current: chain 'H' and resid 324 through 351 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 394 through 409 current: chain 'I' and resid 271 through 287 removed outlier: 6.740A pdb=" N LEU I 331 " --> pdb=" O LEU I 282 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG I 284 " --> pdb=" O GLY I 329 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY I 329 " --> pdb=" O ARG I 284 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL I 286 " --> pdb=" O SER I 327 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N SER I 327 " --> pdb=" O VAL I 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AA5, first strand: chain 'D' and resid 39 through 40 removed outlier: 6.904A pdb=" N SER D 39 " --> pdb=" O CYS D 467 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N CYS D 469 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG D 466 " --> pdb=" O LYS D 463 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AA7, first strand: chain 'D' and resid 123 through 126 removed outlier: 4.649A pdb=" N GLY D 124 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 149 through 151 removed outlier: 3.995A pdb=" N HIS D 149 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 506 through 509 Processing sheet with id=AB1, first strand: chain 'F' and resid 159 through 161 removed outlier: 6.954A pdb=" N LEU F 130 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL F 36 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL F 128 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER F 38 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU F 126 " --> pdb=" O SER F 38 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE F 115 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR F 110 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL F 117 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ARG F 91 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA F 63 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR F 53 " --> pdb=" O LEU F 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AB3, first strand: chain 'E' and resid 26 through 30 Processing sheet with id=AB4, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'E' and resid 133 through 136 removed outlier: 4.657A pdb=" N GLY E 125 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU E 124 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE E 312 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 149 through 151 Processing sheet with id=AB7, first strand: chain 'E' and resid 157 through 161 removed outlier: 3.866A pdb=" N GLU E 157 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG E 166 " --> pdb=" O ASP E 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 477 through 481 Processing sheet with id=AB9, first strand: chain 'E' and resid 525 through 529 Processing sheet with id=AC1, first strand: chain 'A' and resid 80 through 86 removed outlier: 9.110A pdb=" N ASN A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.343A pdb=" N PHE A 31 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 125 through 130 Processing sheet with id=AC4, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.891A pdb=" N THR A 159 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU A 175 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 161 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 173 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 163 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AC6, first strand: chain 'A' and resid 227 through 233 Processing sheet with id=AC7, first strand: chain 'A' and resid 237 through 238 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 237 through 238 current: chain 'A' and resid 289 through 293 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 289 through 293 current: chain 'A' and resid 337 through 341 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AC9, first strand: chain 'A' and resid 362 through 363 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 362 through 363 current: chain 'A' and resid 401 through 403 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 401 through 403 current: chain 'A' and resid 449 through 456 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 464 through 467 Processing sheet with id=AD2, first strand: chain 'A' and resid 481 through 484 Processing sheet with id=AD3, first strand: chain 'A' and resid 508 through 516 removed outlier: 5.261A pdb=" N ILE A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER A 505 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N HIS A 498 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE A 545 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 572 through 575 Processing sheet with id=AD5, first strand: chain 'A' and resid 581 through 582 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 581 through 582 current: chain 'A' and resid 772 through 780 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 772 through 780 current: chain 'A' and resid 808 through 811 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'A' and resid 823 through 827 Processing sheet with id=AD7, first strand: chain 'A' and resid 833 through 834 removed outlier: 6.024A pdb=" N VAL A 833 " --> pdb=" O VAL A 930 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 887 through 888 Processing sheet with id=AD9, first strand: chain 'A' and resid 934 through 944 removed outlier: 4.675A pdb=" N LEU A1356 " --> pdb=" O LEU A 982 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 956 through 959 removed outlier: 5.677A pdb=" N TYR A1317 " --> pdb=" O ALA A1322 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ALA A1322 " --> pdb=" O TYR A1317 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1217 through 1219 removed outlier: 3.711A pdb=" N TYR A1225 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 29 through 33 removed outlier: 6.345A pdb=" N GLN C 29 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER C 51 " --> pdb=" O ASP C 31 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR C 33 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG C 49 " --> pdb=" O TYR C 33 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AE5, first strand: chain 'C' and resid 167 through 169 Processing sheet with id=AE6, first strand: chain 'C' and resid 465 through 469 Processing sheet with id=AE7, first strand: chain 'C' and resid 516 through 520 Processing sheet with id=AE8, first strand: chain 'C' and resid 580 through 582 Processing sheet with id=AE9, first strand: chain 'C' and resid 603 through 606 Processing sheet with id=AF1, first strand: chain 'C' and resid 630 through 631 Processing sheet with id=AF2, first strand: chain 'B' and resid 42 through 47 Processing sheet with id=AF3, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.610A pdb=" N LEU B 83 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 99 through 103 Processing sheet with id=AF5, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.012A pdb=" N SER B 110 " --> pdb=" O CYS B 539 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N CYS B 541 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AF7, first strand: chain 'B' and resid 185 through 186 removed outlier: 6.452A pdb=" N ASN B 185 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 547 through 548 Processing sheet with id=AF9, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AG1, first strand: chain 'B' and resid 644 through 645 Processing sheet with id=AG2, first strand: chain 'B' and resid 653 through 655 Processing sheet with id=AG3, first strand: chain 'B' and resid 676 through 679 Processing sheet with id=AG4, first strand: chain 'B' and resid 703 through 705 Processing sheet with id=AG5, first strand: chain 'B' and resid 727 through 728 Processing sheet with id=AG6, first strand: chain 'H' and resid 23 through 24 Processing sheet with id=AG7, first strand: chain 'H' and resid 39 through 43 Processing sheet with id=AG8, first strand: chain 'H' and resid 84 through 85 Processing sheet with id=AG9, first strand: chain 'H' and resid 127 through 128 removed outlier: 6.635A pdb=" N GLU H 127 " --> pdb=" O ARG H 173 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 497 through 500 Processing sheet with id=AH2, first strand: chain 'I' and resid 23 through 24 removed outlier: 6.161A pdb=" N ARG I 23 " --> pdb=" O GLU I 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 39 through 42 Processing sheet with id=AH4, first strand: chain 'I' and resid 127 through 128 removed outlier: 6.425A pdb=" N GLU I 127 " --> pdb=" O ARG I 173 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 497 through 499 removed outlier: 3.636A pdb=" N THR I 497 " --> pdb=" O ALA I 508 " (cutoff:3.500A) 1152 hydrogen bonds defined for protein. 3102 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: 28.02 Time building geometry restraints manager: 47.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 35650 1.04 - 1.25: 6396 1.25 - 1.46: 14680 1.46 - 1.67: 16597 1.67 - 1.89: 333 Bond restraints: 73656 Sorted by residual: bond pdb=" CA GLY H 426 " pdb=" HA3 GLY H 426 " ideal model delta sigma weight residual 0.970 1.105 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" CA GLY H 426 " pdb=" HA2 GLY H 426 " ideal model delta sigma weight residual 0.970 1.105 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" CA ILE A 905 " pdb=" HA ILE A 905 " ideal model delta sigma weight residual 0.970 1.104 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" CA GLN A 399 " pdb=" HA GLN A 399 " ideal model delta sigma weight residual 0.970 1.104 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" CA LEU D 394 " pdb=" HA LEU D 394 " ideal model delta sigma weight residual 0.970 1.098 -0.128 2.00e-02 2.50e+03 4.12e+01 ... (remaining 73651 not shown) Histogram of bond angle deviations from ideal: 92.37 - 101.14: 47 101.14 - 109.91: 59193 109.91 - 118.68: 40017 118.68 - 127.45: 33032 127.45 - 136.22: 411 Bond angle restraints: 132700 Sorted by residual: angle pdb=" CA PRO E 445 " pdb=" N PRO E 445 " pdb=" CD PRO E 445 " ideal model delta sigma weight residual 112.00 98.37 13.63 1.40e+00 5.10e-01 9.48e+01 angle pdb=" CA PRO B 79 " pdb=" N PRO B 79 " pdb=" CD PRO B 79 " ideal model delta sigma weight residual 112.00 101.04 10.96 1.40e+00 5.10e-01 6.13e+01 angle pdb=" C CYS E 467 " pdb=" CA CYS E 467 " pdb=" CB CYS E 467 " ideal model delta sigma weight residual 110.46 95.53 14.93 1.94e+00 2.66e-01 5.92e+01 angle pdb=" CA PRO I 146 " pdb=" N PRO I 146 " pdb=" CD PRO I 146 " ideal model delta sigma weight residual 112.00 101.98 10.02 1.40e+00 5.10e-01 5.12e+01 angle pdb=" CA CYS C 337 " pdb=" CB CYS C 337 " pdb=" SG CYS C 337 " ideal model delta sigma weight residual 114.40 130.74 -16.34 2.30e+00 1.89e-01 5.05e+01 ... (remaining 132695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 31039 17.97 - 35.94: 2694 35.94 - 53.90: 909 53.90 - 71.87: 452 71.87 - 89.84: 63 Dihedral angle restraints: 35157 sinusoidal: 19069 harmonic: 16088 Sorted by residual: dihedral pdb=" CB CYS E 532 " pdb=" SG CYS E 532 " pdb=" SG CYS E 544 " pdb=" CB CYS E 544 " ideal model delta sinusoidal sigma weight residual 93.00 170.57 -77.57 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS C 103 " pdb=" SG CYS C 103 " pdb=" SG CYS C 119 " pdb=" CB CYS C 119 " ideal model delta sinusoidal sigma weight residual -86.00 -151.17 65.17 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS A 856 " pdb=" SG CYS A 856 " pdb=" SG CYS A 883 " pdb=" CB CYS A 883 " ideal model delta sinusoidal sigma weight residual -86.00 -146.52 60.52 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 35154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 5331 0.113 - 0.226: 179 0.226 - 0.338: 4 0.338 - 0.451: 0 0.451 - 0.564: 1 Chirality restraints: 5515 Sorted by residual: chirality pdb=" CA CYS E 514 " pdb=" N CYS E 514 " pdb=" C CYS E 514 " pdb=" CB CYS E 514 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.95e+00 chirality pdb=" CA CYS B 570 " pdb=" N CYS B 570 " pdb=" C CYS B 570 " pdb=" CB CYS B 570 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA CYS C 337 " pdb=" N CYS C 337 " pdb=" C CYS C 337 " pdb=" CB CYS C 337 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 5512 not shown) Planarity restraints: 11189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 155 " -0.001 2.00e-02 2.50e+03 7.19e-02 1.55e+02 pdb=" CG PHE I 155 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE I 155 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE I 155 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 PHE I 155 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 PHE I 155 " -0.105 2.00e-02 2.50e+03 pdb=" CZ PHE I 155 " 0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE I 155 " 0.128 2.00e-02 2.50e+03 pdb=" HD2 PHE I 155 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE I 155 " -0.054 2.00e-02 2.50e+03 pdb=" HE2 PHE I 155 " 0.119 2.00e-02 2.50e+03 pdb=" HZ PHE I 155 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 418 " 0.201 9.50e-02 1.11e+02 8.73e-02 7.49e+01 pdb=" NE ARG E 418 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG E 418 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG E 418 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG E 418 " -0.109 2.00e-02 2.50e+03 pdb="HH11 ARG E 418 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG E 418 " -0.044 2.00e-02 2.50e+03 pdb="HH21 ARG E 418 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG E 418 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 150 " -0.322 9.50e-02 1.11e+02 1.17e-01 5.94e+01 pdb=" NE ARG B 150 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 150 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG B 150 " 0.074 2.00e-02 2.50e+03 pdb=" NH2 ARG B 150 " 0.052 2.00e-02 2.50e+03 pdb="HH11 ARG B 150 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 150 " -0.063 2.00e-02 2.50e+03 pdb="HH21 ARG B 150 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 150 " -0.053 2.00e-02 2.50e+03 ... (remaining 11186 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.75: 130 1.75 - 2.46: 47131 2.46 - 3.18: 222251 3.18 - 3.89: 285159 3.89 - 4.60: 452777 Nonbonded interactions: 1007448 Sorted by model distance: nonbonded pdb="HD23 LEU D 394 " pdb="HH12 ARG E 414 " model vdw 1.040 2.270 nonbonded pdb="HD23 LEU D 394 " pdb=" NH1 ARG E 414 " model vdw 1.297 2.770 nonbonded pdb="HD23 LEU D 394 " pdb="HH11 ARG E 414 " model vdw 1.320 2.270 nonbonded pdb=" OE1 GLU E 16 " pdb=" H GLU E 16 " model vdw 1.438 1.850 nonbonded pdb=" O VAL H 404 " pdb="HD21 ASN I 190 " model vdw 1.452 1.850 ... (remaining 1007443 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 'H' and (resid 18 through 123 or (resid 124 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 125 through 198 or res \ id 270 through 427 or (resid 428 through 429 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 430 through 521)) selection = (chain 'I' and (resid 18 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 35 through 50 or (resid \ 51 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 52 through 187 or (resid 188 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 189 through 353 or resid 393 or (r \ esid 394 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or \ resid 395 through 419 or (resid 420 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 421 through 491 or (resid 492 and (n \ ame N or name CA or name C or name O or name CB or name SG or name H or name HA \ or name HB2 or name HB3)) or resid 493 through 506 or (resid 507 and (name N or \ name CA or name C or name O or name CB or name SG or name H or name HA or name H \ B2 or name HB3)) or resid 508 through 510 or (resid 511 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 512 through 521)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.26 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: 7.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.810 Extract box with map and model: 31.310 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 180.360 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.240 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: 0.030 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 226.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 37921 Z= 0.275 Angle : 0.873 18.426 51288 Z= 0.492 Chirality : 0.049 0.564 5515 Planarity : 0.010 0.192 6714 Dihedral : 15.384 89.841 14068 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.56 % Allowed : 13.93 % Favored : 85.51 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.12), residues: 4657 helix: -1.65 (0.16), residues: 712 sheet: 0.77 (0.13), residues: 1445 loop : -0.75 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP A1077 HIS 0.025 0.003 HIS B 429 PHE 0.062 0.003 PHE I 155 TYR 0.049 0.007 TYR B 683 ARG 0.024 0.003 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue ILE 429 is missing expected H atoms. Skipping. Evaluate side-chains 816 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 793 time to evaluate : 5.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: G 72 ASN cc_start: 0.6670 (OUTLIER) cc_final: 0.6400 (p0) REVERT: F 165 TYR cc_start: 0.7542 (p90) cc_final: 0.7200 (p90) REVERT: H 128 GLU cc_start: 0.7206 (tt0) cc_final: 0.6105 (tt0) REVERT: I 457 ASN cc_start: 0.9669 (OUTLIER) cc_final: 0.9407 (m110) outliers start: 23 outliers final: 13 residues processed: 805 average time/residue: 1.0898 time to fit residues: 1377.1333 Evaluate side-chains 745 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 730 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 1024 TYR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 457 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 392 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 364 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 271 optimal weight: 0.5980 chunk 422 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 HIS D 233 HIS D 260 HIS D 521 ASN E 51 GLN A 498 HIS ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 37921 Z= 0.332 Angle : 0.638 14.521 51288 Z= 0.345 Chirality : 0.043 0.189 5515 Planarity : 0.005 0.092 6714 Dihedral : 6.838 58.547 5161 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.51 % Allowed : 13.79 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 4657 helix: -0.13 (0.18), residues: 716 sheet: 0.35 (0.13), residues: 1450 loop : -0.44 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 512 HIS 0.010 0.001 HIS G 44 PHE 0.017 0.001 PHE I 52 TYR 0.017 0.002 TYR D 302 ARG 0.008 0.001 ARG A 782 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue ILE 429 is missing expected H atoms. Skipping. Evaluate side-chains 807 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 745 time to evaluate : 4.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 LYS cc_start: 0.7908 (tttm) cc_final: 0.7665 (ttmm) REVERT: F 67 SER cc_start: 0.8698 (m) cc_final: 0.8283 (t) REVERT: F 165 TYR cc_start: 0.7726 (p90) cc_final: 0.7400 (p90) REVERT: E 473 PHE cc_start: 0.8251 (m-80) cc_final: 0.8030 (m-80) REVERT: A 471 ASP cc_start: 0.6753 (t0) cc_final: 0.6238 (p0) REVERT: A 626 PHE cc_start: 0.8638 (t80) cc_final: 0.8415 (t80) REVERT: A 999 ILE cc_start: 0.8978 (mt) cc_final: 0.8473 (tp) REVERT: A 1249 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7483 (mt-10) REVERT: H 313 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: I 463 MET cc_start: 0.8001 (tpp) cc_final: 0.7690 (tpp) outliers start: 62 outliers final: 41 residues processed: 770 average time/residue: 1.0836 time to fit residues: 1293.9652 Evaluate side-chains 747 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 705 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1196 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 313 GLU Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 281 HIS Chi-restraints excluded: chain I residue 502 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 234 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 351 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 423 optimal weight: 9.9990 chunk 456 optimal weight: 10.0000 chunk 376 optimal weight: 5.9990 chunk 419 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 339 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 233 HIS E 51 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 ASN B 26 HIS B 719 GLN I 399 ASN I 450 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 37921 Z= 0.196 Angle : 0.559 13.587 51288 Z= 0.298 Chirality : 0.042 0.181 5515 Planarity : 0.004 0.050 6714 Dihedral : 5.935 56.361 5141 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.68 % Allowed : 13.96 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 4657 helix: 0.48 (0.19), residues: 716 sheet: 0.32 (0.13), residues: 1450 loop : -0.29 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 342 HIS 0.005 0.001 HIS G 44 PHE 0.016 0.001 PHE B 299 TYR 0.018 0.001 TYR A1024 ARG 0.009 0.001 ARG E 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue ILE 429 is missing expected H atoms. Skipping. Evaluate side-chains 823 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 754 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 LYS cc_start: 0.7825 (tttm) cc_final: 0.7603 (ttmm) REVERT: F 67 SER cc_start: 0.8739 (m) cc_final: 0.8297 (t) REVERT: F 165 TYR cc_start: 0.7804 (p90) cc_final: 0.7558 (p90) REVERT: A 323 LEU cc_start: 0.9160 (tp) cc_final: 0.8913 (tp) REVERT: A 324 TYR cc_start: 0.7799 (t80) cc_final: 0.7548 (t80) REVERT: C 374 GLU cc_start: 0.7572 (mp0) cc_final: 0.7309 (mp0) REVERT: B 55 TYR cc_start: 0.7811 (t80) cc_final: 0.7464 (t80) REVERT: B 552 CYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8219 (m) REVERT: B 669 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7866 (tm-30) REVERT: H 94 MET cc_start: 0.8912 (mmt) cc_final: 0.8586 (mmm) REVERT: I 29 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8112 (mm-30) REVERT: I 434 PHE cc_start: 0.6457 (m-80) cc_final: 0.6207 (m-80) REVERT: I 457 ASN cc_start: 0.9577 (OUTLIER) cc_final: 0.9368 (m110) REVERT: I 502 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8659 (p0) outliers start: 69 outliers final: 47 residues processed: 782 average time/residue: 1.0770 time to fit residues: 1307.7469 Evaluate side-chains 768 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 718 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 552 CYS Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 281 HIS Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 457 ASN Chi-restraints excluded: chain I residue 502 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 417 optimal weight: 1.9990 chunk 318 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 284 optimal weight: 0.9980 chunk 424 optimal weight: 0.9980 chunk 449 optimal weight: 7.9990 chunk 221 optimal weight: 0.0870 chunk 402 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 ASN D 233 HIS ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 194 ASN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 37921 Z= 0.233 Angle : 0.550 12.907 51288 Z= 0.293 Chirality : 0.041 0.168 5515 Planarity : 0.004 0.051 6714 Dihedral : 5.583 52.386 5141 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.75 % Allowed : 14.71 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 4657 helix: 0.69 (0.19), residues: 717 sheet: 0.31 (0.13), residues: 1435 loop : -0.25 (0.13), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 568 HIS 0.015 0.001 HIS B 26 PHE 0.016 0.001 PHE H 317 TYR 0.019 0.001 TYR B 55 ARG 0.010 0.000 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue ILE 429 is missing expected H atoms. Skipping. Evaluate side-chains 795 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 723 time to evaluate : 4.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 409 ILE cc_start: 0.9262 (mp) cc_final: 0.8973 (mt) REVERT: F 67 SER cc_start: 0.8823 (m) cc_final: 0.8395 (t) REVERT: F 92 PHE cc_start: 0.8214 (m-80) cc_final: 0.7881 (m-80) REVERT: F 165 TYR cc_start: 0.7834 (p90) cc_final: 0.7625 (p90) REVERT: E 462 MET cc_start: 0.6417 (tpp) cc_final: 0.6159 (tpp) REVERT: A 986 GLU cc_start: 0.8018 (mp0) cc_final: 0.7486 (mp0) REVERT: A 999 ILE cc_start: 0.8927 (mt) cc_final: 0.8558 (tp) REVERT: A 1249 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7380 (mt-10) REVERT: C 374 GLU cc_start: 0.7523 (mp0) cc_final: 0.7261 (mp0) REVERT: C 471 THR cc_start: 0.9099 (p) cc_final: 0.8872 (t) REVERT: B 552 CYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8222 (m) REVERT: B 669 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7912 (tm-30) REVERT: H 94 MET cc_start: 0.8891 (mmt) cc_final: 0.8575 (mmm) REVERT: I 24 MET cc_start: 0.6094 (ttm) cc_final: 0.5356 (ttt) REVERT: I 434 PHE cc_start: 0.6540 (m-80) cc_final: 0.6220 (m-80) REVERT: I 457 ASN cc_start: 0.9581 (OUTLIER) cc_final: 0.9373 (m110) outliers start: 72 outliers final: 56 residues processed: 752 average time/residue: 1.0593 time to fit residues: 1237.8444 Evaluate side-chains 753 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 695 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain E residue 485 CYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 552 CYS Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 281 HIS Chi-restraints excluded: chain I residue 457 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 374 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 334 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 383 optimal weight: 10.0000 chunk 310 optimal weight: 0.2980 chunk 0 optimal weight: 30.0000 chunk 229 optimal weight: 5.9990 chunk 403 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 233 HIS E 51 GLN A 569 ASN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN B 380 GLN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 37921 Z= 0.429 Angle : 0.600 12.368 51288 Z= 0.323 Chirality : 0.043 0.186 5515 Planarity : 0.004 0.064 6714 Dihedral : 5.600 47.977 5139 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.24 % Allowed : 15.07 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.12), residues: 4657 helix: 0.47 (0.19), residues: 722 sheet: 0.14 (0.13), residues: 1401 loop : -0.46 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 342 HIS 0.007 0.001 HIS E 186 PHE 0.020 0.002 PHE B 299 TYR 0.020 0.002 TYR D 302 ARG 0.012 0.001 ARG E 547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue ILE 429 is missing expected H atoms. Skipping. Evaluate side-chains 801 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 709 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 SER cc_start: 0.8858 (m) cc_final: 0.8418 (t) REVERT: F 92 PHE cc_start: 0.8265 (m-80) cc_final: 0.7896 (m-80) REVERT: A 777 VAL cc_start: 0.8781 (t) cc_final: 0.8552 (t) REVERT: A 986 GLU cc_start: 0.8128 (mp0) cc_final: 0.7643 (mp0) REVERT: A 999 ILE cc_start: 0.9070 (mt) cc_final: 0.8640 (tp) REVERT: A 1278 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.6363 (pt0) REVERT: C 471 THR cc_start: 0.9192 (p) cc_final: 0.8955 (t) REVERT: C 487 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: B 304 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 552 CYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8187 (m) REVERT: B 667 ASP cc_start: 0.8571 (p0) cc_final: 0.8268 (p0) REVERT: B 669 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7779 (tm-30) REVERT: H 94 MET cc_start: 0.8916 (mmt) cc_final: 0.8685 (mmm) REVERT: I 51 GLN cc_start: 0.8372 (tp40) cc_final: 0.8073 (tp-100) REVERT: I 407 LEU cc_start: 0.9020 (tt) cc_final: 0.8606 (mt) REVERT: I 434 PHE cc_start: 0.6630 (m-80) cc_final: 0.6400 (m-80) REVERT: I 457 ASN cc_start: 0.9601 (OUTLIER) cc_final: 0.9379 (m110) REVERT: I 483 GLU cc_start: 0.8865 (tt0) cc_final: 0.8483 (tm-30) outliers start: 92 outliers final: 70 residues processed: 757 average time/residue: 1.0676 time to fit residues: 1264.1811 Evaluate side-chains 760 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 686 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 391 SER Chi-restraints excluded: chain E residue 485 CYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1196 SER Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 552 CYS Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 453 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 281 HIS Chi-restraints excluded: chain I residue 457 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 151 optimal weight: 10.0000 chunk 404 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 263 optimal weight: 0.9980 chunk 110 optimal weight: 0.0980 chunk 449 optimal weight: 7.9990 chunk 373 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 403 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 37921 Z= 0.214 Angle : 0.536 12.222 51288 Z= 0.285 Chirality : 0.041 0.167 5515 Planarity : 0.004 0.054 6714 Dihedral : 5.350 45.131 5137 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.58 % Allowed : 16.14 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.12), residues: 4657 helix: 0.76 (0.19), residues: 717 sheet: 0.19 (0.13), residues: 1411 loop : -0.34 (0.13), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 342 HIS 0.005 0.001 HIS E 186 PHE 0.020 0.001 PHE B 299 TYR 0.014 0.001 TYR A1020 ARG 0.012 0.000 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue ILE 429 is missing expected H atoms. Skipping. Evaluate side-chains 787 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 722 time to evaluate : 4.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 SER cc_start: 0.8826 (m) cc_final: 0.8380 (t) REVERT: F 92 PHE cc_start: 0.8119 (m-80) cc_final: 0.7716 (m-80) REVERT: A 777 VAL cc_start: 0.8757 (t) cc_final: 0.8526 (t) REVERT: A 986 GLU cc_start: 0.8174 (mp0) cc_final: 0.7770 (mp0) REVERT: A 999 ILE cc_start: 0.9027 (mt) cc_final: 0.8682 (tp) REVERT: A 1249 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7478 (mt-10) REVERT: B 667 ASP cc_start: 0.8593 (p0) cc_final: 0.8275 (p0) REVERT: B 669 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7885 (tm-30) REVERT: H 94 MET cc_start: 0.8865 (mmt) cc_final: 0.8651 (mmm) REVERT: I 457 ASN cc_start: 0.9586 (OUTLIER) cc_final: 0.9374 (m110) outliers start: 65 outliers final: 50 residues processed: 751 average time/residue: 1.1017 time to fit residues: 1295.0572 Evaluate side-chains 748 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 697 time to evaluate : 4.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 391 SER Chi-restraints excluded: chain E residue 485 CYS Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 313 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 457 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 433 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 256 optimal weight: 0.8980 chunk 328 optimal weight: 0.4980 chunk 254 optimal weight: 0.6980 chunk 378 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 448 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 273 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN B 195 ASN B 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 37921 Z= 0.193 Angle : 0.525 11.947 51288 Z= 0.278 Chirality : 0.041 0.169 5515 Planarity : 0.004 0.049 6714 Dihedral : 5.160 42.522 5137 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.58 % Allowed : 16.61 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.12), residues: 4657 helix: 0.88 (0.19), residues: 717 sheet: 0.25 (0.13), residues: 1415 loop : -0.28 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 342 HIS 0.004 0.001 HIS E 186 PHE 0.021 0.001 PHE B 299 TYR 0.022 0.001 TYR E 28 ARG 0.006 0.000 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue ILE 429 is missing expected H atoms. Skipping. Evaluate side-chains 781 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 716 time to evaluate : 4.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 PHE cc_start: 0.8058 (m-80) cc_final: 0.7639 (m-80) REVERT: A 777 VAL cc_start: 0.8719 (t) cc_final: 0.8469 (t) REVERT: A 986 GLU cc_start: 0.8177 (mp0) cc_final: 0.7843 (mp0) REVERT: A 999 ILE cc_start: 0.9091 (mt) cc_final: 0.8779 (tp) REVERT: A 1022 PHE cc_start: 0.8783 (t80) cc_final: 0.8515 (t80) REVERT: A 1092 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.4801 (m-80) REVERT: A 1249 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7405 (mt-10) REVERT: B 667 ASP cc_start: 0.8577 (p0) cc_final: 0.8249 (p0) REVERT: B 669 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7935 (tm-30) REVERT: I 457 ASN cc_start: 0.9590 (OUTLIER) cc_final: 0.9374 (m110) REVERT: I 478 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9325 (tp30) outliers start: 65 outliers final: 55 residues processed: 746 average time/residue: 1.0196 time to fit residues: 1174.2996 Evaluate side-chains 760 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 703 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 391 SER Chi-restraints excluded: chain E residue 485 CYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1092 TYR Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 313 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain I residue 457 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 277 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 284 optimal weight: 0.0050 chunk 305 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 352 optimal weight: 3.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 146 GLN E 475 ASN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN B 185 ASN B 429 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 37921 Z= 0.218 Angle : 0.524 11.750 51288 Z= 0.278 Chirality : 0.041 0.262 5515 Planarity : 0.004 0.051 6714 Dihedral : 5.059 41.749 5137 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.77 % Allowed : 16.85 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.12), residues: 4657 helix: 0.98 (0.19), residues: 717 sheet: 0.21 (0.13), residues: 1421 loop : -0.29 (0.13), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 342 HIS 0.005 0.001 HIS E 186 PHE 0.036 0.001 PHE A1205 TYR 0.012 0.001 TYR D 302 ARG 0.009 0.000 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue ILE 429 is missing expected H atoms. Skipping. Evaluate side-chains 782 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 709 time to evaluate : 4.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 SER cc_start: 0.8813 (m) cc_final: 0.8345 (t) REVERT: F 92 PHE cc_start: 0.8094 (m-80) cc_final: 0.7646 (m-80) REVERT: E 408 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8290 (ttp-110) REVERT: A 176 GLU cc_start: 0.8164 (tp30) cc_final: 0.7914 (tp30) REVERT: A 777 VAL cc_start: 0.8769 (t) cc_final: 0.8523 (t) REVERT: A 986 GLU cc_start: 0.8210 (mp0) cc_final: 0.7894 (mp0) REVERT: A 999 ILE cc_start: 0.9112 (mt) cc_final: 0.8888 (tp) REVERT: A 1022 PHE cc_start: 0.8780 (t80) cc_final: 0.8515 (t80) REVERT: A 1092 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.4762 (m-80) REVERT: A 1249 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7436 (mt-10) REVERT: B 667 ASP cc_start: 0.8575 (p0) cc_final: 0.8230 (p0) REVERT: B 669 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7955 (tm-30) REVERT: I 457 ASN cc_start: 0.9592 (OUTLIER) cc_final: 0.9389 (m110) REVERT: I 478 GLU cc_start: 0.9656 (mm-30) cc_final: 0.9295 (tp30) outliers start: 73 outliers final: 62 residues processed: 748 average time/residue: 1.0523 time to fit residues: 1217.8589 Evaluate side-chains 763 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 699 time to evaluate : 4.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 391 SER Chi-restraints excluded: chain E residue 485 CYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1092 TYR Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 457 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 407 optimal weight: 0.3980 chunk 429 optimal weight: 20.0000 chunk 391 optimal weight: 4.9990 chunk 417 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 327 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 395 optimal weight: 0.9980 chunk 416 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN B 185 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 37921 Z= 0.310 Angle : 0.551 11.578 51288 Z= 0.293 Chirality : 0.042 0.194 5515 Planarity : 0.004 0.055 6714 Dihedral : 5.083 41.382 5137 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.82 % Allowed : 16.95 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.12), residues: 4657 helix: 0.88 (0.19), residues: 718 sheet: 0.13 (0.13), residues: 1433 loop : -0.35 (0.13), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 342 HIS 0.006 0.001 HIS E 186 PHE 0.021 0.001 PHE B 299 TYR 0.016 0.001 TYR D 302 ARG 0.006 0.000 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue ILE 429 is missing expected H atoms. Skipping. Evaluate side-chains 775 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 700 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 67 SER cc_start: 0.8827 (m) cc_final: 0.8341 (t) REVERT: F 92 PHE cc_start: 0.8159 (m-80) cc_final: 0.7756 (m-80) REVERT: E 166 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6801 (ttt-90) REVERT: E 408 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8321 (ttp-110) REVERT: E 494 LEU cc_start: 0.9284 (tt) cc_final: 0.9082 (tt) REVERT: A 176 GLU cc_start: 0.8197 (tp30) cc_final: 0.7961 (tp30) REVERT: A 777 VAL cc_start: 0.8806 (t) cc_final: 0.8566 (t) REVERT: A 986 GLU cc_start: 0.8258 (mp0) cc_final: 0.7946 (mp0) REVERT: A 999 ILE cc_start: 0.9153 (mt) cc_final: 0.8793 (tp) REVERT: A 1022 PHE cc_start: 0.8809 (t80) cc_final: 0.8551 (t80) REVERT: A 1092 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.4817 (m-80) REVERT: A 1249 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7447 (mt-10) REVERT: A 1278 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6541 (pt0) REVERT: C 663 MET cc_start: -0.2267 (ttt) cc_final: -0.2605 (ttp) REVERT: B 667 ASP cc_start: 0.8574 (p0) cc_final: 0.8221 (p0) REVERT: B 669 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8018 (tm-30) REVERT: H 272 MET cc_start: 0.8275 (tpp) cc_final: 0.7807 (tpp) REVERT: I 407 LEU cc_start: 0.8915 (tt) cc_final: 0.8695 (mt) REVERT: I 457 ASN cc_start: 0.9588 (OUTLIER) cc_final: 0.9368 (m110) REVERT: I 478 GLU cc_start: 0.9655 (mm-30) cc_final: 0.9418 (tp30) outliers start: 75 outliers final: 69 residues processed: 740 average time/residue: 1.0840 time to fit residues: 1251.5859 Evaluate side-chains 767 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 694 time to evaluate : 4.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 391 SER Chi-restraints excluded: chain E residue 485 CYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1092 TYR Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 313 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain I residue 457 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 274 optimal weight: 0.9980 chunk 441 optimal weight: 0.9990 chunk 269 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 463 optimal weight: 20.0000 chunk 426 optimal weight: 0.0970 chunk 368 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 284 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 146 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37921 Z= 0.203 Angle : 0.530 11.619 51288 Z= 0.280 Chirality : 0.041 0.180 5515 Planarity : 0.004 0.055 6714 Dihedral : 4.983 41.042 5137 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.58 % Allowed : 17.29 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.12), residues: 4657 helix: 0.98 (0.19), residues: 718 sheet: 0.15 (0.13), residues: 1448 loop : -0.30 (0.13), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 342 HIS 0.005 0.001 HIS E 186 PHE 0.034 0.001 PHE A 246 TYR 0.013 0.001 TYR A1020 ARG 0.008 0.000 ARG B 693 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9314 Ramachandran restraints generated. 4657 Oldfield, 0 Emsley, 4657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 264 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue VAL 428 is missing expected H atoms. Skipping. Residue ILE 429 is missing expected H atoms. Skipping. Evaluate side-chains 784 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 719 time to evaluate : 4.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 447 SER cc_start: 0.9031 (t) cc_final: 0.8800 (t) REVERT: F 67 SER cc_start: 0.8810 (m) cc_final: 0.8326 (t) REVERT: F 92 PHE cc_start: 0.8125 (m-80) cc_final: 0.7598 (m-80) REVERT: E 277 ASP cc_start: 0.7524 (t70) cc_final: 0.7292 (t70) REVERT: E 408 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8277 (ttp-110) REVERT: A 176 GLU cc_start: 0.8202 (tp30) cc_final: 0.7935 (tp30) REVERT: A 185 PHE cc_start: 0.8752 (m-80) cc_final: 0.8521 (m-80) REVERT: A 777 VAL cc_start: 0.8764 (t) cc_final: 0.8517 (t) REVERT: A 986 GLU cc_start: 0.8271 (mp0) cc_final: 0.7979 (mp0) REVERT: A 999 ILE cc_start: 0.9149 (mt) cc_final: 0.8920 (tp) REVERT: A 1022 PHE cc_start: 0.8767 (t80) cc_final: 0.8492 (t80) REVERT: A 1092 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.4801 (m-80) REVERT: A 1249 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7437 (mt-10) REVERT: C 663 MET cc_start: -0.2283 (ttt) cc_final: -0.2623 (ttp) REVERT: B 667 ASP cc_start: 0.8537 (p0) cc_final: 0.8191 (p0) REVERT: B 669 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8006 (tm-30) REVERT: I 457 ASN cc_start: 0.9580 (OUTLIER) cc_final: 0.9369 (m110) REVERT: I 478 GLU cc_start: 0.9652 (mm-30) cc_final: 0.9285 (tp30) outliers start: 65 outliers final: 59 residues processed: 753 average time/residue: 1.0257 time to fit residues: 1202.3122 Evaluate side-chains 763 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 702 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 56 HIS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 391 SER Chi-restraints excluded: chain E residue 485 CYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1092 TYR Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain I residue 457 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 293 optimal weight: 0.3980 chunk 392 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 340 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 369 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 379 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 455 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.184604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125144 restraints weight = 171770.502| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.77 r_work: 0.3198 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37921 Z= 0.211 Angle : 0.532 15.123 51288 Z= 0.280 Chirality : 0.041 0.176 5515 Planarity : 0.004 0.057 6714 Dihedral : 4.955 41.157 5137 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.58 % Allowed : 17.38 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 4657 helix: 1.00 (0.19), residues: 724 sheet: 0.15 (0.13), residues: 1446 loop : -0.28 (0.13), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 342 HIS 0.005 0.001 HIS E 186 PHE 0.024 0.001 PHE A 246 TYR 0.012 0.001 TYR A1020 ARG 0.013 0.000 ARG B 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21324.16 seconds wall clock time: 368 minutes 20.64 seconds (22100.64 seconds total)