Starting phenix.real_space_refine on Sun Mar 17 14:15:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0g_15780/03_2024/8b0g_15780_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0g_15780/03_2024/8b0g_15780.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/8b0g_15780/03_2024/8b0g_15780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0g_15780/03_2024/8b0g_15780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0g_15780/03_2024/8b0g_15780_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0g_15780/03_2024/8b0g_15780_trim.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= 0.003 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 622 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 297 5.16 5 C 25372 2.51 5 N 6970 2.21 5 O 7842 1.98 5 H 38789 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 105": "OE1" <-> "OE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C ASP 320": "OD1" <-> "OD2" Residue "C ASP 328": "OD1" <-> "OD2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 133": "OD1" <-> "OD2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E ASP 388": "OD1" <-> "OD2" Residue "E GLU 531": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F ASP 178": "OD1" <-> "OD2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 279": "OE1" <-> "OE2" Residue "H GLU 319": "OE1" <-> "OE2" Residue "H PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 538": "OE1" <-> "OE2" Residue "B TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B ASP 634": "OD1" <-> "OD2" Residue "J ASP 123": "OD1" <-> "OD2" Residue "J GLU 198": "OE1" <-> "OE2" Residue "I PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 163": "OD1" <-> "OD2" Residue "I GLU 319": "OE1" <-> "OE2" Residue "I TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 402": "OD1" <-> "OD2" Residue "I ASP 433": "OD1" <-> "OD2" Residue "I GLU 519": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 79270 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 19687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 19687 Classifications: {'peptide': 1245} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1186} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: "D" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 8096 Classifications: {'peptide': 518} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 494} Chain breaks: 2 Chain: "E" Number of atoms: 7865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 7865 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: "F" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2603 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain: "H" Number of atoms: 6301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6301 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 15, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 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: "J" Number of atoms: 6135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6135 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 15, 'TRANS': 383} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6203 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1211 Classifications: {'peptide': 78} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N MET G 0 " occ=0.47 ... (17 atoms not shown) pdb=" HE3 MET G 0 " occ=0.47 residue: pdb=" N GLN G 2 " occ=0.35 ... (15 atoms not shown) pdb="HE22 GLN G 2 " occ=0.35 residue: pdb=" N PHE G 23 " occ=0.49 ... (18 atoms not shown) pdb=" HZ PHE G 23 " occ=0.49 residue: pdb=" N THR G 52 " occ=0.36 ... (12 atoms not shown) pdb="HG23 THR G 52 " occ=0.36 Time building chain proxies: 27.22, per 1000 atoms: 0.34 Number of scatterers: 79270 At special positions: 0 Unit cell: (122.988, 194.454, 262.596, 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 297 16.00 O 7842 8.00 N 6970 7.00 C 25372 6.00 H 38789 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=108, symmetry=0 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=2.02 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=2.03 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=2.03 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=2.05 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 D 11 " - pdb=" SG CYS D 46 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 56 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 62 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 101 " distance=2.04 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 146 " distance=2.04 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 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 164 " - pdb=" SG CYS F 40 " distance=2.03 Simple disulfide: pdb=" SG CYS E 345 " - pdb=" SG CYS E 369 " distance=2.03 Simple disulfide: pdb=" SG CYS E 467 " - pdb=" SG CYS E 514 " distance=2.04 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 F 76 " - pdb=" SG CYS F 168 " distance=2.02 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=2.03 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=2.02 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 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=2.03 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=2.04 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=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 732 " - pdb=" SG CYS B 761 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 57 " distance=2.03 Simple disulfide: pdb=" SG CYS J 33 " - pdb=" SG CYS J 67 " distance=2.03 Simple disulfide: pdb=" SG CYS J 36 " - pdb=" SG CYS J 73 " distance=2.03 Simple disulfide: pdb=" SG CYS J 80 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 86 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 98 " - pdb=" SG CYS J 113 " distance=2.03 Simple disulfide: pdb=" SG CYS J 121 " - pdb=" SG CYS J 160 " distance=2.03 Simple disulfide: pdb=" SG CYS J 489 " - pdb=" SG CYS J 505 " distance=2.03 Simple disulfide: pdb=" SG CYS J 492 " - pdb=" SG CYS J 507 " distance=2.03 Simple disulfide: pdb=" SG CYS J 509 " - pdb=" SG CYS J 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=2.03 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=2.03 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 492 " - pdb=" SG CYS I 507 " distance=2.03 Simple disulfide: pdb=" SG CYS I 509 " - pdb=" SG CYS I 518 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 69 " distance=2.02 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 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG K 1 " - " ASN A 911 " " NAG L 1 " - " ASN D 189 " " NAG M 1 " - " ASN E 407 " " NAG N 1 " - " ASN H 394 " " NAG O 1 " - " ASN B 324 " Time building additional restraints: 49.17 Conformation dependent library (CDL) restraints added in 6.1 seconds 10118 Ramachandran restraints generated. 5059 Oldfield, 0 Emsley, 5059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9490 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 73 sheets defined 20.1% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.76 Creating SS restraints... Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 239 through 245 removed outlier: 4.231A pdb=" N LYS A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN A 245 " --> pdb=" O LYS A 241 " (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 492 through 497 removed outlier: 4.046A pdb=" N THR A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.663A pdb=" N GLN A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 641 through 649 Processing helix chain 'A' and resid 994 through 1001 removed outlier: 3.909A pdb=" N ASN A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1027 Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 3.592A pdb=" N ASN A1032 " --> pdb=" O GLY A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1037 Processing helix chain 'A' and resid 1041 through 1060 Processing helix chain 'A' and resid 1075 through 1090 removed outlier: 3.795A pdb=" N ASN A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1112 removed outlier: 3.582A pdb=" N ILE A1100 " --> pdb=" O ASN A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1157 removed outlier: 4.106A 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 Processing helix chain 'A' and resid 1202 through 1216 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 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.742A pdb=" N GLY C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 273 through 282 Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.650A 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 removed outlier: 3.587A pdb=" N LEU C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) 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 546 through 557 removed outlier: 4.012A pdb=" N LEU C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 561 Processing helix chain 'D' and resid 117 through 122 removed outlier: 3.622A pdb=" N LEU D 121 " --> pdb=" O GLY D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 275 through 287 removed outlier: 4.075A 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 403 removed outlier: 3.733A pdb=" N GLN D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 427 through 446 removed outlier: 3.559A pdb=" N LYS D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 451 removed outlier: 3.570A pdb=" N HIS D 450 " --> pdb=" O SER D 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 removed outlier: 4.277A pdb=" N ALA E 64 " --> pdb=" O VAL E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 118 through 123 removed outlier: 4.360A pdb=" N ALA E 122 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 118 through 123' Processing helix chain 'E' and resid 281 through 291 removed outlier: 3.579A pdb=" N LEU E 291 " --> pdb=" O SER E 287 " (cutoff:3.500A) 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 420 Processing helix chain 'E' and resid 435 through 441 removed outlier: 4.287A pdb=" N ARG E 439 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS E 440 " --> pdb=" O GLU E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 461 Processing helix chain 'E' and resid 465 through 469 Processing helix chain 'F' and resid 23 through 28 Processing helix chain 'F' and resid 40 through 44 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 'H' and resid 93 through 97 Processing helix chain 'H' and resid 104 through 106 No H-bonds generated for 'chain 'H' and resid 104 through 106' Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 129 through 135 Processing helix chain 'H' and resid 295 through 304 Processing helix chain 'H' and resid 310 through 322 Processing helix chain 'H' and resid 412 through 425 Processing helix chain 'H' and resid 430 through 441 removed outlier: 3.598A 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 removed outlier: 3.726A pdb=" N LYS H 488 " --> pdb=" O SER H 485 " (cutoff:3.500A) 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 removed outlier: 3.669A pdb=" N ILE B 64 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 65 " --> pdb=" O CYS B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 60 through 65' Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 335 through 345 Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.739A pdb=" N ILE B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 358 " --> pdb=" O TYR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 465 through 479 Processing helix chain 'B' and resid 491 through 494 Processing helix chain 'B' and resid 499 through 519 Processing helix chain 'B' and resid 520 through 523 Processing helix chain 'J' and resid 93 through 100 removed outlier: 3.530A pdb=" N CYS J 98 " --> pdb=" O ARG J 95 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY J 100 " --> pdb=" O ARG J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 113 Processing helix chain 'J' and resid 131 through 135 Processing helix chain 'J' and resid 295 through 305 Processing helix chain 'J' and resid 310 through 322 Processing helix chain 'J' and resid 342 through 350 Processing helix chain 'J' and resid 353 through 361 Processing helix chain 'J' and resid 412 through 425 removed outlier: 3.580A pdb=" N ARG J 425 " --> pdb=" O GLU J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 444 removed outlier: 3.723A pdb=" N ASN J 442 " --> pdb=" O ALA J 438 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP J 443 " --> pdb=" O SER J 439 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 459 Processing helix chain 'J' and resid 465 through 485 Processing helix chain 'J' and resid 486 through 489 Processing helix chain 'I' and resid 95 through 97 No H-bonds generated for 'chain 'I' and resid 95 through 97' Processing helix chain 'I' and resid 129 through 135 Processing helix chain 'I' and resid 295 through 305 Processing helix chain 'I' and resid 310 through 322 Processing helix chain 'I' and resid 412 through 425 Processing helix chain 'I' and resid 430 through 442 removed outlier: 4.027A 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 helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 71 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 removed outlier: 9.067A pdb=" N ASN A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.326A pdb=" N PHE A 31 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.750A pdb=" N ASP A 172 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 233 removed outlier: 3.668A pdb=" N LYS A 258 " --> pdb=" O TYR A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 238 removed outlier: 5.782A pdb=" N LEU A 323 " --> pdb=" O GLY A 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 362 through 363 removed outlier: 5.133A pdb=" N ALA A 392 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ASP A 405 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A 394 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASP A 403 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 464 through 467 Processing sheet with id=AB2, first strand: chain 'A' and resid 481 through 484 removed outlier: 3.572A pdb=" N ILE A 484 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 508 through 516 removed outlier: 5.121A pdb=" N ILE A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER A 505 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N HIS A 498 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE A 545 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 572 through 575 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 572 through 575 current: chain 'A' and resid 772 through 789 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 772 through 789 current: chain 'A' and resid 808 through 811 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 823 through 827 removed outlier: 3.504A pdb=" N PHE A 824 " --> pdb=" O TYR A 846 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 826 " --> pdb=" O THR A 844 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 833 through 834 removed outlier: 6.219A pdb=" N VAL A 833 " --> pdb=" O VAL A 930 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 853 through 854 Processing sheet with id=AB8, first strand: chain 'A' and resid 934 through 944 Processing sheet with id=AB9, first strand: chain 'A' and resid 956 through 959 removed outlier: 5.730A pdb=" N TYR A1317 " --> pdb=" O ALA A1322 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ALA A1322 " --> pdb=" O TYR A1317 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1217 through 1219 removed outlier: 3.789A pdb=" N TYR A1225 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 29 through 33 removed outlier: 6.584A pdb=" N GLN C 29 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER C 51 " --> pdb=" O ASP C 31 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR C 33 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG C 49 " --> pdb=" O TYR C 33 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.123A pdb=" N GLY C 56 " --> pdb=" O CYS C 473 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N CYS C 475 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AC5, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.785A pdb=" N GLY C 143 " --> pdb=" O ARG C 152 " (cutoff:3.500A) 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: 3.849A pdb=" N SER C 232 " --> pdb=" O LYS C 335 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU C 309 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA C 260 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY C 307 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE C 262 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN C 305 " --> pdb=" O PHE C 262 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 348 through 373 current: chain 'D' and resid 213 through 252 removed outlier: 5.024A pdb=" N ILE D 214 " --> pdb=" O LYS D 330 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS D 330 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER D 216 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASP D 328 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER D 218 " --> pdb=" O LYS D 326 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS D 326 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG D 220 " --> pdb=" O CYS D 324 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS D 324 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS D 222 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N HIS D 322 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR D 224 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN D 320 " --> pdb=" O TYR D 224 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ARG D 226 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU D 318 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N THR D 228 " --> pdb=" O TYR D 316 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR D 316 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ARG D 230 " --> pdb=" O GLY D 314 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY D 314 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER D 232 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU D 312 " --> pdb=" O SER D 232 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR D 234 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA D 310 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER D 236 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS D 308 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE D 238 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N MET D 306 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N HIS D 240 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU D 304 " --> pdb=" O HIS D 240 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG D 242 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR D 302 " --> pdb=" O ARG D 242 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP D 244 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N TYR D 300 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU D 246 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY D 298 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR D 292 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 346 " --> pdb=" O ASN D 327 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 343 through 374 current: chain 'E' and resid 240 through 273 removed outlier: 6.234A pdb=" N MET E 317 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS E 270 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY E 315 " --> pdb=" O HIS E 270 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS E 272 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N THR E 313 " --> pdb=" O LYS E 272 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 370 through 374 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 262 through 287 removed outlier: 6.704A pdb=" N LEU H 331 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG H 284 " --> pdb=" O GLY H 329 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY H 329 " --> pdb=" O ARG H 284 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL H 286 " --> pdb=" O SER H 327 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N SER H 327 " --> pdb=" O VAL H 286 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 394 through 409 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: 6.745A pdb=" N LEU B 371 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASN B 324 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY B 369 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR B 326 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR B 367 " --> pdb=" O THR B 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 413 through 445 current: chain 'J' and resid 271 through 287 removed outlier: 4.860A pdb=" N PHE J 273 " --> pdb=" O LEU J 341 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU J 341 " --> pdb=" O PHE J 273 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N HIS J 275 " --> pdb=" O TYR J 339 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR J 339 " --> pdb=" O HIS J 275 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LYS J 277 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU J 337 " --> pdb=" O LYS J 277 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLU J 279 " --> pdb=" O TYR J 335 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR J 335 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS J 281 " --> pdb=" O GLY J 333 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY J 333 " --> pdb=" O HIS J 281 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER J 327 " --> pdb=" O MET J 287 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE J 338 " --> pdb=" O VAL J 405 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 405 through 409 current: chain 'I' and resid 145 through 147 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 145 through 147 current: chain 'I' and resid 262 through 287 removed outlier: 6.618A pdb=" N LEU I 331 " --> pdb=" O LEU I 282 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG I 284 " --> pdb=" O GLY I 329 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY I 329 " --> pdb=" O ARG I 284 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL I 286 " --> pdb=" O SER I 327 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N SER I 327 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN I 399 " --> pdb=" O ALA I 344 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 399 through 409 current: chain 'G' and resid 35 through 40 Processing sheet with id=AC6, first strand: chain 'C' and resid 167 through 170 Processing sheet with id=AC7, first strand: chain 'C' and resid 481 through 482 Processing sheet with id=AC8, first strand: chain 'C' and resid 516 through 520 Processing sheet with id=AC9, first strand: chain 'C' and resid 570 through 571 removed outlier: 4.478A pdb=" N PHE C 589 " --> pdb=" O CYS C 571 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 580 through 582 Processing sheet with id=AD2, first strand: chain 'C' and resid 603 through 606 Processing sheet with id=AD3, first strand: chain 'C' and resid 631 through 632 Processing sheet with id=AD4, first strand: chain 'C' and resid 641 through 642 Processing sheet with id=AD5, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AD6, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AD7, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD8, first strand: chain 'D' and resid 123 through 126 removed outlier: 4.442A pdb=" N GLY D 124 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 149 through 151 removed outlier: 3.778A pdb=" N HIS D 149 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 459 through 462 Processing sheet with id=AE2, first strand: chain 'D' and resid 506 through 509 Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AE4, first strand: chain 'E' and resid 26 through 30 Processing sheet with id=AE5, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AE6, first strand: chain 'E' and resid 124 through 126 removed outlier: 5.437A pdb=" N GLN E 135 " --> pdb=" O GLY E 125 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 149 through 151 Processing sheet with id=AE8, first strand: chain 'E' and resid 158 through 160 Processing sheet with id=AE9, first strand: chain 'E' and resid 477 through 481 Processing sheet with id=AF1, first strand: chain 'E' and resid 493 through 494 removed outlier: 3.673A pdb=" N GLN E 500 " --> pdb=" O LEU E 494 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 525 through 529 Processing sheet with id=AF3, first strand: chain 'F' and resid 159 through 161 removed outlier: 6.651A pdb=" N LEU F 130 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL F 36 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL F 128 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE F 115 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR F 110 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL F 117 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR F 53 " --> pdb=" O LEU F 33 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 39 through 43 Processing sheet with id=AF5, first strand: chain 'H' and resid 84 through 85 Processing sheet with id=AF6, first strand: chain 'H' and resid 162 through 164 Processing sheet with id=AF7, first strand: chain 'H' and resid 497 through 500 Processing sheet with id=AF8, first strand: chain 'B' and resid 42 through 47 Processing sheet with id=AF9, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.460A pdb=" N LEU B 83 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 99 through 103 Processing sheet with id=AG2, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AG3, first strand: chain 'B' and resid 185 through 186 removed outlier: 6.656A pdb=" N ASN B 185 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 531 through 534 Processing sheet with id=AG5, first strand: chain 'B' and resid 547 through 548 Processing sheet with id=AG6, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AG7, first strand: chain 'B' and resid 644 through 645 Processing sheet with id=AG8, first strand: chain 'B' and resid 653 through 655 Processing sheet with id=AG9, first strand: chain 'B' and resid 676 through 680 Processing sheet with id=AH1, first strand: chain 'B' and resid 704 through 705 Processing sheet with id=AH2, first strand: chain 'B' and resid 727 through 729 Processing sheet with id=AH3, first strand: chain 'J' and resid 23 through 33 removed outlier: 8.075A pdb=" N SER J 25 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLU J 47 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP J 27 " --> pdb=" O SER J 45 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER J 45 " --> pdb=" O TRP J 27 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE J 41 " --> pdb=" O SER J 31 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N CYS J 33 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLN J 39 " --> pdb=" O CYS J 33 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 127 through 128 removed outlier: 6.872A pdb=" N GLU J 127 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 497 through 501 Processing sheet with id=AH6, first strand: chain 'I' and resid 39 through 43 Processing sheet with id=AH7, first strand: chain 'I' and resid 83 through 85 Processing sheet with id=AH8, first strand: chain 'I' and resid 162 through 164 Processing sheet with id=AH9, first strand: chain 'I' and resid 497 through 500 Processing sheet with id=AI1, first strand: chain 'G' and resid 2 through 4 1304 hydrogen bonds defined for protein. 3555 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: 31.49 Time building geometry restraints manager: 51.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.25: 45089 1.25 - 1.68: 34677 1.68 - 2.10: 372 2.10 - 2.53: 0 2.53 - 2.96: 1 Bond restraints: 80139 Sorted by residual: bond pdb=" C GLY J 350 " pdb=" N GLU J 352 " ideal model delta sigma weight residual 1.332 2.959 -1.627 1.40e-02 5.10e+03 1.35e+04 bond pdb=" N GLN A 399 " pdb=" H GLN A 399 " ideal model delta sigma weight residual 0.860 1.019 -0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" CA GLN A 399 " pdb=" HA GLN A 399 " ideal model delta sigma weight residual 0.970 1.105 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" CA ASP D 393 " pdb=" HA ASP D 393 " ideal model delta sigma weight residual 0.970 1.104 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" CA GLY H 426 " pdb=" HA3 GLY H 426 " ideal model delta sigma weight residual 0.970 1.104 -0.134 2.00e-02 2.50e+03 4.47e+01 ... (remaining 80134 not shown) Histogram of bond angle deviations from ideal: 18.99 - 44.00: 1 44.00 - 69.01: 0 69.01 - 94.02: 7 94.02 - 119.04: 108797 119.04 - 144.05: 35499 Bond angle restraints: 144304 Sorted by residual: angle pdb=" C ASN A 398 " pdb=" N GLN A 399 " pdb=" H GLN A 399 " ideal model delta sigma weight residual 123.20 18.99 104.21 3.00e+00 1.11e-01 1.21e+03 angle pdb=" O GLY J 350 " pdb=" C GLY J 350 " pdb=" N GLU J 352 " ideal model delta sigma weight residual 122.70 144.05 -21.35 1.30e+00 5.92e-01 2.70e+02 angle pdb=" CA GLY J 350 " pdb=" C GLY J 350 " pdb=" N GLU J 352 " ideal model delta sigma weight residual 116.69 93.73 22.96 2.04e+00 2.40e-01 1.27e+02 angle pdb=" CG2 VAL E 437 " pdb=" CB VAL E 437 " pdb=" HB VAL E 437 " ideal model delta sigma weight residual 108.00 81.82 26.18 3.00e+00 1.11e-01 7.62e+01 angle pdb=" CG1 VAL E 437 " pdb=" CB VAL E 437 " pdb=" HB VAL E 437 " ideal model delta sigma weight residual 108.00 81.94 26.06 3.00e+00 1.11e-01 7.54e+01 ... (remaining 144299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.96: 34767 19.96 - 39.92: 2400 39.92 - 59.88: 929 59.88 - 79.85: 265 79.85 - 99.81: 31 Dihedral angle restraints: 38392 sinusoidal: 20910 harmonic: 17482 Sorted by residual: dihedral pdb=" CA GLY J 350 " pdb=" C GLY J 350 " pdb=" N GLU J 352 " pdb=" CA GLU J 352 " ideal model delta harmonic sigma weight residual -180.00 -80.19 -99.81 0 5.00e+00 4.00e-02 3.98e+02 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 93.00 170.42 -77.42 1 1.00e+01 1.00e-02 7.51e+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 93.00 152.72 -59.72 1 1.00e+01 1.00e-02 4.76e+01 ... (remaining 38389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.771: 6040 0.771 - 1.542: 1 1.542 - 2.314: 1 2.314 - 3.085: 0 3.085 - 3.856: 1 Chirality restraints: 6043 Sorted by residual: chirality pdb=" C2 NAG N 2 " pdb=" C1 NAG N 2 " pdb=" C3 NAG N 2 " pdb=" N2 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.49 1.36 -3.86 2.00e-01 2.50e+01 3.72e+02 chirality pdb=" CG LEU E 206 " pdb=" CB LEU E 206 " pdb=" CD1 LEU E 206 " pdb=" CD2 LEU E 206 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.76e+01 chirality pdb=" CB VAL E 437 " pdb=" CA VAL E 437 " pdb=" CG1 VAL E 437 " pdb=" CG2 VAL E 437 " both_signs ideal model delta sigma weight residual False -2.63 -1.18 -1.45 2.00e-01 2.50e+01 5.22e+01 ... (remaining 6040 not shown) Planarity restraints: 12181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 70 " -0.130 9.50e-02 1.11e+02 6.96e-02 6.88e+01 pdb=" NE ARG F 70 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG F 70 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG F 70 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG F 70 " 0.104 2.00e-02 2.50e+03 pdb="HH11 ARG F 70 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 70 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG F 70 " 0.006 2.00e-02 2.50e+03 pdb="HH22 ARG F 70 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS G 6 " -0.137 5.00e-02 4.00e+02 1.98e-01 6.27e+01 pdb=" N PRO G 7 " 0.342 5.00e-02 4.00e+02 pdb=" CA PRO G 7 " -0.115 5.00e-02 4.00e+02 pdb=" CD PRO G 7 " -0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 466 " -0.497 9.50e-02 1.11e+02 1.70e-01 5.82e+01 pdb=" NE ARG D 466 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG D 466 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG D 466 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG D 466 " 0.067 2.00e-02 2.50e+03 pdb="HH11 ARG D 466 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG D 466 " -0.025 2.00e-02 2.50e+03 pdb="HH21 ARG D 466 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG D 466 " -0.069 2.00e-02 2.50e+03 ... (remaining 12178 not shown) Histogram of nonbonded interaction distances: 0.95 - 1.68: 116 1.68 - 2.41: 37359 2.41 - 3.14: 243609 3.14 - 3.87: 314697 3.87 - 4.60: 508862 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1104643 Sorted by model distance: nonbonded pdb="HD23 LEU D 394 " pdb="HH12 ARG E 414 " model vdw 0.949 2.270 nonbonded pdb=" O ASN A 398 " pdb=" H GLN A 399 " model vdw 1.253 1.960 nonbonded pdb=" OD1 ASP A 131 " pdb=" HH TYR A 135 " model vdw 1.464 1.850 nonbonded pdb=" OE1 GLU B 629 " pdb=" H GLU B 629 " model vdw 1.465 1.850 nonbonded pdb=" OE1 GLU A 986 " pdb=" H GLU A 986 " model vdw 1.475 1.850 ... (remaining 1104638 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 342 or (resid 343 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 344 through 346 or (resid 347 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 348 \ through 350 or resid 352 through 353 or resid 398 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 re \ sid 421 through 427 or (resid 428 through 429 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 430 through 461 or (resid 4 \ 62 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 463 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 123 or (resid \ 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 198 or resid 270 through 342 or (resid 343 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 344 th \ rough 346 or (resid 347 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 348 through 350 or resid 352 through 427 or (resi \ d 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 'J' 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 96 or (resid 97 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 98 through 353 or resid 398 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 461 or (resid 462 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 463 through 510 or \ (resid 511 through 512 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 513 through 521)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=0.14 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: 6.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.380 Construct map_model_manager: 0.930 Extract box with map and model: 31.890 Check model and map are aligned: 0.890 Set scattering table: 0.610 Process input model: 196.560 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.350 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 242.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.009 1.627 41350 Z= 0.513 Angle : 0.801 22.963 55917 Z= 0.455 Chirality : 0.074 3.856 6043 Planarity : 0.010 0.198 7309 Dihedral : 14.550 99.808 15499 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.34 % Allowed : 8.89 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.94 (0.11), residues: 5059 helix: -1.72 (0.15), residues: 824 sheet: 0.50 (0.12), residues: 1544 loop : -0.90 (0.11), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP A1077 HIS 0.023 0.003 HIS F 175 PHE 0.030 0.003 PHE E 199 TYR 0.060 0.007 TYR F 165 ARG 0.047 0.003 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10118 Ramachandran restraints generated. 5059 Oldfield, 0 Emsley, 5059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10118 Ramachandran restraints generated. 5059 Oldfield, 0 Emsley, 5059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 264 is missing expected H atoms. Skipping. Residue LYS 512 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 343 is missing expected H atoms. Skipping. Residue LYS 347 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. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue LYS 512 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 5.066 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: C 326 GLN cc_start: 0.7268 (pt0) cc_final: 0.6894 (tm-30) REVERT: D 194 MET cc_start: 0.6886 (mmp) cc_final: 0.6361 (mmp) REVERT: J 287 MET cc_start: 0.8825 (mmm) cc_final: 0.8336 (mmm) outliers start: 15 outliers final: 8 residues processed: 174 average time/residue: 1.0472 time to fit residues: 295.2134 Evaluate side-chains 154 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 223 HIS Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 426 optimal weight: 8.9990 chunk 382 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 395 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 458 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS ** A1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1360 HIS C 368 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41350 Z= 0.237 Angle : 0.610 15.130 55917 Z= 0.330 Chirality : 0.051 1.713 6043 Planarity : 0.004 0.097 7309 Dihedral : 6.739 55.074 5805 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.37 % Favored : 97.59 % Rotamer: Outliers : 0.78 % Allowed : 8.19 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.34 (0.11), residues: 5061 helix: -0.23 (0.17), residues: 859 sheet: 0.20 (0.12), residues: 1553 loop : -0.39 (0.12), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1077 HIS 0.006 0.001 HIS D 380 PHE 0.015 0.001 PHE D 442 TYR 0.020 0.002 TYR H 480 ARG 0.006 0.000 ARG E 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 264 is missing expected H atoms. Skipping. Residue LYS 512 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 343 is missing expected H atoms. Skipping. Residue LYS 347 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. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue LYS 512 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 5.251 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: A 596 MET cc_start: 0.7402 (pmm) cc_final: 0.7052 (pmm) REVERT: D 194 MET cc_start: 0.7233 (mmt) cc_final: 0.6721 (mmp) REVERT: H 40 MET cc_start: 0.8695 (ptp) cc_final: 0.8286 (ptp) REVERT: B 552 CYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7493 (m) REVERT: B 704 CYS cc_start: 0.3953 (OUTLIER) cc_final: 0.2826 (m) REVERT: J 287 MET cc_start: 0.9168 (mmm) cc_final: 0.8564 (mmm) outliers start: 35 outliers final: 18 residues processed: 182 average time/residue: 1.0165 time to fit residues: 306.4540 Evaluate side-chains 162 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 5.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain H residue 446 VAL Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 552 CYS Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 501 MET Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 501 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 254 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 381 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 459 optimal weight: 6.9990 chunk 496 optimal weight: 4.9990 chunk 409 optimal weight: 9.9990 chunk 455 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 368 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 HIS ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS E 423 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN I 471 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 41350 Z= 0.418 Angle : 0.614 13.761 55917 Z= 0.333 Chirality : 0.052 1.716 6043 Planarity : 0.004 0.063 7309 Dihedral : 6.223 52.321 5796 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.01 % Allowed : 8.98 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 5061 helix: 0.06 (0.17), residues: 853 sheet: -0.10 (0.12), residues: 1549 loop : -0.42 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 560 HIS 0.010 0.001 HIS D 380 PHE 0.021 0.001 PHE D 442 TYR 0.022 0.002 TYR D 302 ARG 0.012 0.001 ARG J 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 264 is missing expected H atoms. Skipping. Residue LYS 512 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 343 is missing expected H atoms. Skipping. Residue LYS 347 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. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue LYS 512 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 5.217 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: J 287 MET cc_start: 0.9237 (mmm) cc_final: 0.8468 (mmm) REVERT: I 483 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6918 (tp30) outliers start: 45 outliers final: 27 residues processed: 181 average time/residue: 1.0423 time to fit residues: 311.6398 Evaluate side-chains 162 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 5.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain H residue 446 VAL Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain I residue 501 MET Chi-restraints excluded: chain G residue 29 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 453 optimal weight: 10.0000 chunk 345 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 chunk 461 optimal weight: 9.9990 chunk 488 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 436 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 HIS ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 41350 Z= 0.450 Angle : 0.618 14.620 55917 Z= 0.335 Chirality : 0.052 1.724 6043 Planarity : 0.004 0.061 7309 Dihedral : 6.032 47.333 5796 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.23 % Allowed : 9.49 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.11), residues: 5061 helix: 0.06 (0.17), residues: 850 sheet: -0.37 (0.12), residues: 1578 loop : -0.58 (0.12), residues: 2633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 560 HIS 0.008 0.001 HIS H 275 PHE 0.019 0.001 PHE D 442 TYR 0.020 0.002 TYR D 302 ARG 0.010 0.001 ARG D 510 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 264 is missing expected H atoms. Skipping. Residue LYS 512 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 343 is missing expected H atoms. Skipping. Residue LYS 347 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. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue LYS 512 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 138 time to evaluate : 5.058 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: A 625 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8579 (pp30) REVERT: D 410 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8010 (tttt) REVERT: H 40 MET cc_start: 0.8802 (ptp) cc_final: 0.8578 (ptp) REVERT: B 704 CYS cc_start: 0.5053 (OUTLIER) cc_final: 0.4039 (m) REVERT: I 483 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7240 (tp30) outliers start: 55 outliers final: 39 residues processed: 187 average time/residue: 1.0356 time to fit residues: 317.7191 Evaluate side-chains 176 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 133 time to evaluate : 5.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 472 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 446 VAL Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain I residue 501 MET Chi-restraints excluded: chain G residue 29 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 406 optimal weight: 0.9990 chunk 277 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 363 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 416 optimal weight: 40.0000 chunk 337 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 438 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 41350 Z= 0.160 Angle : 0.522 14.433 55917 Z= 0.279 Chirality : 0.050 1.710 6043 Planarity : 0.003 0.055 7309 Dihedral : 5.637 47.345 5796 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.85 % Allowed : 10.28 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 5061 helix: 0.47 (0.18), residues: 857 sheet: -0.21 (0.12), residues: 1575 loop : -0.34 (0.12), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 560 HIS 0.005 0.001 HIS A 498 PHE 0.012 0.001 PHE D 442 TYR 0.016 0.001 TYR D 302 ARG 0.003 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 264 is missing expected H atoms. Skipping. Residue LYS 512 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 343 is missing expected H atoms. Skipping. Residue LYS 347 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. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue LYS 512 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 5.171 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: H 169 LEU cc_start: 0.7415 (mm) cc_final: 0.7176 (tp) REVERT: I 483 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7121 (tp30) outliers start: 38 outliers final: 29 residues processed: 166 average time/residue: 1.0544 time to fit residues: 285.5893 Evaluate side-chains 159 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 4.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 472 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain H residue 446 VAL Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain I residue 501 MET Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 57 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 164 optimal weight: 1.9990 chunk 439 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 488 optimal weight: 6.9990 chunk 405 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 HIS B 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 41350 Z= 0.356 Angle : 0.565 14.600 55917 Z= 0.303 Chirality : 0.050 1.722 6043 Planarity : 0.004 0.097 7309 Dihedral : 5.535 50.186 5794 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.21 % Allowed : 10.30 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.11), residues: 5061 helix: 0.51 (0.18), residues: 848 sheet: -0.36 (0.12), residues: 1591 loop : -0.42 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 560 HIS 0.007 0.001 HIS A 498 PHE 0.016 0.001 PHE D 442 TYR 0.016 0.002 TYR D 302 ARG 0.009 0.000 ARG D 510 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 264 is missing expected H atoms. Skipping. Residue LYS 512 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 343 is missing expected H atoms. Skipping. Residue LYS 347 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. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue LYS 512 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 135 time to evaluate : 5.089 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: A 312 TYR cc_start: 0.7621 (p90) cc_final: 0.7256 (p90) REVERT: A 1013 MET cc_start: 0.7405 (mtt) cc_final: 0.7096 (mtt) REVERT: D 68 CYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6735 (t) REVERT: J 287 MET cc_start: 0.8869 (mmm) cc_final: 0.8235 (mmm) REVERT: J 336 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: I 483 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7226 (tp30) outliers start: 54 outliers final: 42 residues processed: 182 average time/residue: 1.0623 time to fit residues: 319.7602 Evaluate side-chains 178 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 133 time to evaluate : 5.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain A residue 1247 MET Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 472 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain H residue 446 VAL Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain G residue 29 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 471 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 356 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 chunk 411 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 486 optimal weight: 0.8980 chunk 304 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A1032 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 41350 Z= 0.192 Angle : 0.509 14.524 55917 Z= 0.272 Chirality : 0.050 1.705 6043 Planarity : 0.003 0.057 7309 Dihedral : 5.305 51.507 5794 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.87 % Allowed : 10.81 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.12), residues: 5061 helix: 0.75 (0.18), residues: 847 sheet: -0.28 (0.12), residues: 1588 loop : -0.29 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 560 HIS 0.004 0.001 HIS A 498 PHE 0.011 0.001 PHE D 442 TYR 0.014 0.001 TYR D 302 ARG 0.003 0.000 ARG D 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 264 is missing expected H atoms. Skipping. Residue LYS 512 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 343 is missing expected H atoms. Skipping. Residue LYS 347 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. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue LYS 512 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 5.151 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: A 312 TYR cc_start: 0.7604 (p90) cc_final: 0.7222 (p90) REVERT: A 853 MET cc_start: 0.8627 (ttp) cc_final: 0.8413 (tmm) REVERT: A 1013 MET cc_start: 0.7373 (mtt) cc_final: 0.7086 (mtt) REVERT: H 169 LEU cc_start: 0.7427 (mm) cc_final: 0.7188 (tp) REVERT: J 287 MET cc_start: 0.9010 (mmm) cc_final: 0.8430 (mmm) REVERT: J 336 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: I 483 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7156 (tp30) outliers start: 39 outliers final: 36 residues processed: 175 average time/residue: 1.0667 time to fit residues: 309.5516 Evaluate side-chains 174 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 5.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 472 HIS Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain H residue 446 VAL Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 291 ASP Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 57 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 301 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 309 optimal weight: 8.9990 chunk 331 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 382 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 ASN A1292 ASN ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 41350 Z= 0.478 Angle : 0.595 14.542 55917 Z= 0.321 Chirality : 0.051 1.736 6043 Planarity : 0.004 0.067 7309 Dihedral : 5.463 53.081 5793 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.30 % Allowed : 10.72 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.56 (0.12), residues: 5061 helix: 0.47 (0.18), residues: 847 sheet: -0.46 (0.12), residues: 1604 loop : -0.48 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 560 HIS 0.008 0.001 HIS H 275 PHE 0.019 0.001 PHE D 442 TYR 0.019 0.002 TYR D 302 ARG 0.011 0.001 ARG D 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 264 is missing expected H atoms. Skipping. Residue LYS 512 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 343 is missing expected H atoms. Skipping. Residue LYS 347 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. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue LYS 512 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 136 time to evaluate : 5.116 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: A 312 TYR cc_start: 0.7569 (p90) cc_final: 0.7229 (p90) REVERT: A 853 MET cc_start: 0.8649 (ttp) cc_final: 0.8431 (tmm) REVERT: A 1013 MET cc_start: 0.7524 (mtt) cc_final: 0.7219 (mtt) REVERT: D 68 CYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6813 (t) REVERT: D 410 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7920 (tttt) REVERT: J 287 MET cc_start: 0.9080 (mmm) cc_final: 0.8245 (mmm) REVERT: J 336 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: I 483 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7377 (tp30) outliers start: 58 outliers final: 46 residues processed: 188 average time/residue: 1.0482 time to fit residues: 327.3009 Evaluate side-chains 186 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 136 time to evaluate : 5.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 472 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain H residue 446 VAL Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain J residue 24 MET Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 291 ASP Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain G residue 29 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 442 optimal weight: 10.0000 chunk 466 optimal weight: 5.9990 chunk 425 optimal weight: 10.0000 chunk 453 optimal weight: 9.9990 chunk 273 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 356 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 409 optimal weight: 9.9990 chunk 428 optimal weight: 8.9990 chunk 451 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN C 608 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 41350 Z= 0.287 Angle : 0.533 14.470 55917 Z= 0.286 Chirality : 0.050 1.718 6043 Planarity : 0.004 0.058 7309 Dihedral : 5.321 54.669 5791 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.28 % Allowed : 10.72 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.45 (0.12), residues: 5061 helix: 0.60 (0.18), residues: 848 sheet: -0.38 (0.12), residues: 1587 loop : -0.43 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 560 HIS 0.005 0.001 HIS A 498 PHE 0.013 0.001 PHE D 442 TYR 0.016 0.001 TYR D 302 ARG 0.006 0.000 ARG D 510 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 264 is missing expected H atoms. Skipping. Residue LYS 512 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 343 is missing expected H atoms. Skipping. Residue LYS 347 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. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue LYS 512 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 139 time to evaluate : 5.158 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: A 312 TYR cc_start: 0.7563 (p90) cc_final: 0.7238 (p90) REVERT: A 853 MET cc_start: 0.8640 (ttp) cc_final: 0.8412 (tmm) REVERT: D 7 MET cc_start: 0.7821 (tpt) cc_final: 0.7569 (mmm) REVERT: D 68 CYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6865 (t) REVERT: D 410 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7882 (tttt) REVERT: B 704 CYS cc_start: 0.5161 (OUTLIER) cc_final: 0.4092 (m) REVERT: J 287 MET cc_start: 0.9020 (mmm) cc_final: 0.8229 (mmm) REVERT: J 336 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: I 483 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7370 (tp30) outliers start: 57 outliers final: 48 residues processed: 189 average time/residue: 1.0346 time to fit residues: 323.1048 Evaluate side-chains 187 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 134 time to evaluate : 5.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 472 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 446 VAL Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 291 ASP Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 341 LEU Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 57 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 297 optimal weight: 9.9990 chunk 479 optimal weight: 1.9990 chunk 292 optimal weight: 8.9990 chunk 227 optimal weight: 0.6980 chunk 333 optimal weight: 10.0000 chunk 503 optimal weight: 0.9980 chunk 463 optimal weight: 6.9990 chunk 400 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 309 optimal weight: 8.9990 chunk 245 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 41350 Z= 0.280 Angle : 0.619 59.197 55917 Z= 0.346 Chirality : 0.050 1.718 6043 Planarity : 0.004 0.058 7309 Dihedral : 5.317 54.641 5791 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.19 % Allowed : 10.84 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.44 (0.12), residues: 5061 helix: 0.60 (0.18), residues: 848 sheet: -0.39 (0.12), residues: 1597 loop : -0.42 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 560 HIS 0.005 0.001 HIS A 498 PHE 0.013 0.001 PHE D 442 TYR 0.016 0.001 TYR G 4 ARG 0.008 0.000 ARG H 164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10122 Ramachandran restraints generated. 5061 Oldfield, 0 Emsley, 5061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 264 is missing expected H atoms. Skipping. Residue LYS 512 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 343 is missing expected H atoms. Skipping. Residue LYS 347 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. Residue LYS 420 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue LYS 512 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 134 time to evaluate : 5.127 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: A 312 TYR cc_start: 0.7567 (p90) cc_final: 0.7248 (p90) REVERT: A 853 MET cc_start: 0.8639 (ttp) cc_final: 0.8411 (tmm) REVERT: D 7 MET cc_start: 0.7820 (tpt) cc_final: 0.7568 (mmm) REVERT: D 68 CYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6864 (t) REVERT: D 410 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7880 (tttt) REVERT: B 704 CYS cc_start: 0.5160 (OUTLIER) cc_final: 0.4092 (m) REVERT: J 287 MET cc_start: 0.9020 (mmm) cc_final: 0.8236 (mmm) REVERT: J 336 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: I 483 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7370 (tp30) outliers start: 53 outliers final: 47 residues processed: 181 average time/residue: 1.0551 time to fit residues: 316.2182 Evaluate side-chains 186 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 134 time to evaluate : 6.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 1022 PHE Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 472 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 446 VAL Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 291 ASP Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 341 LEU Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 57 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 318 optimal weight: 0.9980 chunk 426 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 369 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 401 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 412 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.092812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.058989 restraints weight = 376567.826| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.46 r_work: 0.2948 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 41350 Z= 0.280 Angle : 0.619 59.197 55917 Z= 0.346 Chirality : 0.050 1.718 6043 Planarity : 0.004 0.058 7309 Dihedral : 5.317 54.641 5791 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.16 % Allowed : 10.86 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.44 (0.12), residues: 5061 helix: 0.60 (0.18), residues: 848 sheet: -0.39 (0.12), residues: 1597 loop : -0.42 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 560 HIS 0.005 0.001 HIS A 498 PHE 0.013 0.001 PHE D 442 TYR 0.016 0.001 TYR G 4 ARG 0.008 0.000 ARG H 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12750.51 seconds wall clock time: 223 minutes 44.93 seconds (13424.93 seconds total)