Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 16:44:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0g_15780/10_2023/8b0g_15780_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0g_15780/10_2023/8b0g_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_15780/10_2023/8b0g_15780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0g_15780/10_2023/8b0g_15780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0g_15780/10_2023/8b0g_15780_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0g_15780/10_2023/8b0g_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-1.21rc1-5097/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 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 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 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 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 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: 25.74, per 1000 atoms: 0.32 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: 52.37 Conformation dependent library (CDL) restraints added in 5.1 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: 4.14 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: 33.06 Time building geometry restraints manager: 55.24 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: 29727 19.96 - 39.92: 1939 39.92 - 59.88: 580 59.88 - 79.85: 264 79.85 - 99.81: 28 Dihedral angle restraints: 32538 sinusoidal: 15056 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 32535 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: 9.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.360 Construct map_model_manager: 0.940 Extract box with map and model: 32.100 Check model and map are aligned: 0.910 Set scattering table: 0.580 Process input model: 201.410 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 250.430 ------------------------------------------------------------------------------- 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 15289 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 *********************** 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 : 5.166 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 outliers start: 15 outliers final: 8 residues processed: 174 average time/residue: 1.1001 time to fit residues: 311.5717 Evaluate side-chains 153 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 5.096 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 8 average time/residue: 0.8757 time to fit residues: 18.6263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 426 optimal weight: 10.0000 chunk 382 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 395 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 458 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41350 Z= 0.204 Angle : 0.605 14.590 55917 Z= 0.326 Chirality : 0.051 1.710 6043 Planarity : 0.004 0.098 7309 Dihedral : 6.405 50.911 5579 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.65 % Rotamer: Outliers : 0.74 % Allowed : 8.08 % Favored : 91.18 % 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: -0.29 (0.11), residues: 5061 helix: -0.18 (0.17), residues: 859 sheet: 0.25 (0.12), residues: 1546 loop : -0.36 (0.12), residues: 2656 *********************** 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 187 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 5.076 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 outliers start: 33 outliers final: 18 residues processed: 180 average time/residue: 1.0302 time to fit residues: 306.9838 Evaluate side-chains 158 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 5.032 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 18 average time/residue: 0.9138 time to fit residues: 34.3232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 381 optimal weight: 3.9990 chunk 312 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 459 optimal weight: 5.9990 chunk 496 optimal weight: 20.0000 chunk 409 optimal weight: 10.0000 chunk 455 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 chunk 368 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 HIS C 368 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS E 423 ASN B 44 GLN I 471 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 41350 Z= 0.451 Angle : 0.644 13.823 55917 Z= 0.348 Chirality : 0.052 1.717 6043 Planarity : 0.004 0.065 7309 Dihedral : 6.013 49.094 5579 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.89 % Rotamer: Outliers : 0.96 % Allowed : 9.09 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.11), residues: 5061 helix: -0.03 (0.17), residues: 853 sheet: -0.19 (0.12), residues: 1555 loop : -0.49 (0.12), residues: 2653 *********************** 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 185 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 5.053 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 outliers start: 43 outliers final: 25 residues processed: 179 average time/residue: 1.0222 time to fit residues: 303.6249 Evaluate side-chains 159 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 4.939 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 5 residues processed: 25 average time/residue: 0.7461 time to fit residues: 40.3248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 453 optimal weight: 9.9990 chunk 345 optimal weight: 6.9990 chunk 238 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 308 optimal weight: 0.6980 chunk 461 optimal weight: 9.9990 chunk 488 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 436 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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** D 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41350 Z= 0.295 Angle : 0.568 14.479 55917 Z= 0.305 Chirality : 0.051 1.712 6043 Planarity : 0.003 0.054 7309 Dihedral : 5.652 39.821 5579 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.58 % Allowed : 9.58 % Favored : 89.84 % 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: 0.25 (0.17), residues: 857 sheet: -0.19 (0.12), residues: 1555 loop : -0.43 (0.12), residues: 2649 *********************** 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 166 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 4.991 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 outliers start: 26 outliers final: 14 residues processed: 160 average time/residue: 1.1081 time to fit residues: 291.9641 Evaluate side-chains 148 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 5.122 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 14 average time/residue: 0.8542 time to fit residues: 27.5937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 406 optimal weight: 8.9990 chunk 277 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 chunk 363 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 416 optimal weight: 0.1980 chunk 337 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 438 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** B 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 41350 Z= 0.144 Angle : 0.511 14.346 55917 Z= 0.271 Chirality : 0.050 1.707 6043 Planarity : 0.003 0.057 7309 Dihedral : 5.217 39.932 5579 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.49 % Allowed : 9.49 % 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: -0.17 (0.11), residues: 5061 helix: 0.61 (0.18), residues: 857 sheet: -0.09 (0.12), residues: 1532 loop : -0.27 (0.12), residues: 2672 *********************** 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 159 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 5.061 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 outliers start: 22 outliers final: 14 residues processed: 154 average time/residue: 1.0931 time to fit residues: 273.4155 Evaluate side-chains 147 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 5.031 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 14 average time/residue: 0.8555 time to fit residues: 26.9517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 164 optimal weight: 0.0980 chunk 439 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 488 optimal weight: 9.9990 chunk 405 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41350 Z= 0.262 Angle : 0.530 14.639 55917 Z= 0.282 Chirality : 0.050 1.713 6043 Planarity : 0.003 0.058 7309 Dihedral : 5.150 38.846 5579 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.27 % Allowed : 10.30 % Favored : 89.43 % 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: -0.22 (0.12), residues: 5061 helix: 0.67 (0.18), residues: 855 sheet: -0.18 (0.12), residues: 1577 loop : -0.28 (0.12), residues: 2629 *********************** 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 149 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 5.180 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 outliers start: 12 outliers final: 7 residues processed: 147 average time/residue: 1.0730 time to fit residues: 257.9424 Evaluate side-chains 141 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 5.060 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 0.8144 time to fit residues: 16.9974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 471 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 356 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 411 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 486 optimal weight: 1.9990 chunk 304 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** A1292 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41350 Z= 0.191 Angle : 0.506 14.418 55917 Z= 0.267 Chirality : 0.050 1.703 6043 Planarity : 0.003 0.060 7309 Dihedral : 4.940 36.187 5579 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.40 % Allowed : 10.50 % Favored : 89.10 % 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: -0.12 (0.12), residues: 5061 helix: 0.82 (0.18), residues: 854 sheet: -0.15 (0.12), residues: 1567 loop : -0.23 (0.12), residues: 2640 *********************** 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 160 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 5.140 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 outliers start: 18 outliers final: 8 residues processed: 155 average time/residue: 1.0910 time to fit residues: 277.9876 Evaluate side-chains 143 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 5.084 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 8 average time/residue: 0.8794 time to fit residues: 18.5298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 301 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 290 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 309 optimal weight: 10.0000 chunk 331 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 382 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 41350 Z= 0.353 Angle : 0.547 14.587 55917 Z= 0.292 Chirality : 0.050 1.724 6043 Planarity : 0.003 0.061 7309 Dihedral : 5.024 35.008 5579 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.31 % Allowed : 10.70 % Favored : 88.99 % 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: -0.24 (0.12), residues: 5061 helix: 0.74 (0.18), residues: 854 sheet: -0.21 (0.12), residues: 1563 loop : -0.33 (0.12), residues: 2644 *********************** 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 151 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 5.092 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 outliers start: 14 outliers final: 9 residues processed: 149 average time/residue: 1.0829 time to fit residues: 263.3112 Evaluate side-chains 144 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 5.085 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 9 average time/residue: 0.8156 time to fit residues: 19.0798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 425 optimal weight: 10.0000 chunk 453 optimal weight: 9.9990 chunk 273 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 356 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 409 optimal weight: 10.0000 chunk 428 optimal weight: 10.0000 chunk 451 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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** A 625 GLN ** 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 41350 Z= 0.359 Angle : 0.560 14.393 55917 Z= 0.300 Chirality : 0.051 1.730 6043 Planarity : 0.004 0.063 7309 Dihedral : 5.104 31.125 5579 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.27 % Allowed : 10.86 % Favored : 88.87 % 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: -0.40 (0.12), residues: 5061 helix: 0.61 (0.18), residues: 848 sheet: -0.32 (0.12), residues: 1576 loop : -0.42 (0.12), residues: 2637 *********************** 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 143 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 5.244 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 outliers start: 12 outliers final: 9 residues processed: 140 average time/residue: 1.0989 time to fit residues: 251.4844 Evaluate side-chains 139 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 5.028 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 9 average time/residue: 0.8308 time to fit residues: 19.6129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 292 optimal weight: 7.9990 chunk 227 optimal weight: 0.3980 chunk 333 optimal weight: 2.9990 chunk 503 optimal weight: 2.9990 chunk 463 optimal weight: 6.9990 chunk 400 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 245 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 ASN A1130 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 41350 Z= 0.237 Angle : 0.518 14.514 55917 Z= 0.275 Chirality : 0.050 1.712 6043 Planarity : 0.003 0.062 7309 Dihedral : 4.975 29.878 5579 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.18 % Allowed : 10.95 % Favored : 88.87 % 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: -0.28 (0.12), residues: 5061 helix: 0.78 (0.18), residues: 846 sheet: -0.27 (0.12), residues: 1578 loop : -0.35 (0.12), residues: 2637 ********************** 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 140 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 5.170 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 outliers start: 8 outliers final: 7 residues processed: 136 average time/residue: 1.0872 time to fit residues: 242.3331 Evaluate side-chains 137 residues out of total 4499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 5.040 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 7 average time/residue: 0.8473 time to fit residues: 16.6149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 318 optimal weight: 1.9990 chunk 426 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 369 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 412 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 700 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.092435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.059277 restraints weight = 376449.728| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.30 r_work: 0.2931 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 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 = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 41350 Z= 0.362 Angle : 0.559 14.578 55917 Z= 0.298 Chirality : 0.050 1.734 6043 Planarity : 0.004 0.063 7309 Dihedral : 5.044 29.718 5579 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.20 % Allowed : 11.04 % Favored : 88.76 % 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: -0.45 (0.12), residues: 5061 helix: 0.67 (0.18), residues: 841 sheet: -0.40 (0.13), residues: 1577 loop : -0.46 (0.12), residues: 2643 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12057.78 seconds wall clock time: 211 minutes 45.99 seconds (12705.99 seconds total)