Starting phenix.real_space_refine on Sun Feb 18 11:03:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/02_2024/7um0_24763_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/02_2024/7um0_24763.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/02_2024/7um0_24763_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/02_2024/7um0_24763_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/02_2024/7um0_24763_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/02_2024/7um0_24763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/02_2024/7um0_24763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/02_2024/7um0_24763_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/02_2024/7um0_24763_updated.pdb" } resolution = 3.8 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= 1.000 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 60 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3 5.49 5 S 81 5.16 5 C 13924 2.51 5 N 3547 2.21 5 O 4204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 33": "OD1" <-> "OD2" Residue "d PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 49": "OD1" <-> "OD2" Residue "d ASP 51": "OD1" <-> "OD2" Residue "d TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 105": "OE1" <-> "OE2" Residue "d PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 122": "OD1" <-> "OD2" Residue "d GLU 126": "OE1" <-> "OE2" Residue "d TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 139": "OD1" <-> "OD2" Residue "d PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 143": "OE1" <-> "OE2" Residue "d PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 178": "OE1" <-> "OE2" Residue "d TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 188": "OE1" <-> "OE2" Residue "d TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 228": "OE1" <-> "OE2" Residue "d PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 263": "OD1" <-> "OD2" Residue "d TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 274": "OE1" <-> "OE2" Residue "d TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 294": "OE1" <-> "OE2" Residue "d PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 370": "OD1" <-> "OD2" Residue "d PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 383": "OD1" <-> "OD2" Residue "d ASP 401": "OD1" <-> "OD2" Residue "d PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 412": "OD1" <-> "OD2" Residue "d ASP 416": "OD1" <-> "OD2" Residue "c TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 73": "OE1" <-> "OE2" Residue "c ASP 89": "OD1" <-> "OD2" Residue "c PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 155": "OD1" <-> "OD2" Residue "c PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 198": "OD1" <-> "OD2" Residue "c ASP 207": "OD1" <-> "OD2" Residue "c GLU 215": "OE1" <-> "OE2" Residue "c PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 233": "OD1" <-> "OD2" Residue "c PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 260": "OD1" <-> "OD2" Residue "c TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 285": "OE1" <-> "OE2" Residue "c GLU 288": "OE1" <-> "OE2" Residue "c ARG 296": "NH1" <-> "NH2" Residue "c ARG 307": "NH1" <-> "NH2" Residue "c GLU 310": "OE1" <-> "OE2" Residue "c ARG 344": "NH1" <-> "NH2" Residue "c PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 363": "NH1" <-> "NH2" Residue "c PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 399": "NH1" <-> "NH2" Residue "c TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 401": "OD1" <-> "OD2" Residue "c PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 454": "OD1" <-> "OD2" Residue "c PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 469": "OE1" <-> "OE2" Residue "c PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 477": "OE1" <-> "OE2" Residue "c GLU 480": "OE1" <-> "OE2" Residue "D TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 206": "OD1" <-> "OD2" Residue "D ASP 228": "OD1" <-> "OD2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 354": "OE1" <-> "OE2" Residue "D ASP 370": "OD1" <-> "OD2" Residue "D TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 435": "OD1" <-> "OD2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 472": "OD1" <-> "OD2" Residue "D ASP 478": "OD1" <-> "OD2" Residue "D PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 497": "OD1" <-> "OD2" Residue "D ASP 500": "OD1" <-> "OD2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 563": "OE1" <-> "OE2" Residue "D ASP 578": "OD1" <-> "OD2" Residue "D ASP 582": "OD1" <-> "OD2" Residue "D PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 605": "OE1" <-> "OE2" Residue "D ASP 615": "OD1" <-> "OD2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2": "OD1" <-> "OD2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 204": "OD1" <-> "OD2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 351": "OE1" <-> "OE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C ASP 382": "OD1" <-> "OD2" Residue "C ASP 383": "OD1" <-> "OD2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 399": "OD1" <-> "OD2" Residue "C ARG 429": "NH1" <-> "NH2" Residue "C ASP 431": "OD1" <-> "OD2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 478": "OD1" <-> "OD2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 605": "NH1" <-> "NH2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C ASP 619": "OD1" <-> "OD2" Residue "C ASP 623": "OD1" <-> "OD2" Residue "C GLU 628": "OE1" <-> "OE2" Residue "C ASP 648": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21760 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3814 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 451} Chain: "d" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3488 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 412} Chain: "c" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 4003 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain: "D" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5123 Classifications: {'peptide': 629} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 614} Chain: "C" Number of atoms: 5271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5271 Classifications: {'peptide': 649} Link IDs: {'PTRANS': 18, 'TRANS': 630} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13674 SG CYS D 294 42.337 66.383 96.664 1.00 97.98 S ATOM 14117 SG CYS D 350 42.387 65.810 93.230 1.00 89.24 S ATOM 14188 SG CYS D 360 40.777 62.541 94.460 1.00 67.26 S Time building chain proxies: 11.66, per 1000 atoms: 0.54 Number of scatterers: 21760 At special positions: 0 Unit cell: (144.72, 166.32, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 81 16.00 P 3 15.00 O 4204 8.00 N 3547 7.00 C 13924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.82 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 360 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 294 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 350 " 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 21 sheets defined 39.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 21 through 24 No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 49 through 58 Processing helix chain 'A' and resid 62 through 77 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 98 through 108 Processing helix chain 'A' and resid 133 through 154 Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 160 through 178 removed outlier: 3.589A pdb=" N LYS A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.782A pdb=" N THR A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 212 removed outlier: 4.109A pdb=" N LYS A 212 " --> pdb=" O TRP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 282 through 288 Processing helix chain 'A' and resid 296 through 315 Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 354 through 370 Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.708A pdb=" N SER A 413 " --> pdb=" O TYR A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 426 through 433 removed outlier: 4.060A pdb=" N ILE A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 Processing helix chain 'd' and resid 10 through 13 No H-bonds generated for 'chain 'd' and resid 10 through 13' Processing helix chain 'd' and resid 70 through 79 removed outlier: 4.545A pdb=" N THR d 74 " --> pdb=" O PRO d 70 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE d 75 " --> pdb=" O ILE d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 117 No H-bonds generated for 'chain 'd' and resid 114 through 117' Processing helix chain 'd' and resid 121 through 128 removed outlier: 4.264A pdb=" N GLU d 126 " --> pdb=" O ASP d 122 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS d 127 " --> pdb=" O ASP d 123 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR d 128 " --> pdb=" O LEU d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 135 through 143 removed outlier: 3.541A pdb=" N ILE d 142 " --> pdb=" O TYR d 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 148 No H-bonds generated for 'chain 'd' and resid 146 through 148' Processing helix chain 'd' and resid 178 through 192 removed outlier: 3.998A pdb=" N VAL d 186 " --> pdb=" O TYR d 183 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE d 187 " --> pdb=" O ASN d 184 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE d 190 " --> pdb=" O ILE d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 226 Proline residue: d 209 - end of helix removed outlier: 3.537A pdb=" N TYR d 212 " --> pdb=" O LEU d 208 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU d 222 " --> pdb=" O ALA d 218 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 239 No H-bonds generated for 'chain 'd' and resid 236 through 239' Processing helix chain 'd' and resid 269 through 275 Processing helix chain 'd' and resid 277 through 288 removed outlier: 3.670A pdb=" N LYS d 286 " --> pdb=" O ASN d 282 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL d 287 " --> pdb=" O LEU d 283 " (cutoff:3.500A) Processing helix chain 'd' and resid 292 through 304 removed outlier: 3.833A pdb=" N LYS d 297 " --> pdb=" O ASN d 293 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE d 298 " --> pdb=" O GLU d 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU d 304 " --> pdb=" O GLU d 300 " (cutoff:3.500A) Processing helix chain 'd' and resid 309 through 320 removed outlier: 3.769A pdb=" N TYR d 313 " --> pdb=" O GLU d 309 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU d 316 " --> pdb=" O ASN d 312 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE d 318 " --> pdb=" O MET d 314 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR d 319 " --> pdb=" O GLU d 315 " (cutoff:3.500A) Processing helix chain 'd' and resid 362 through 367 Processing helix chain 'd' and resid 384 through 393 removed outlier: 3.880A pdb=" N GLU d 388 " --> pdb=" O ASN d 384 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS d 389 " --> pdb=" O LYS d 385 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU d 392 " --> pdb=" O GLU d 388 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU d 393 " --> pdb=" O HIS d 389 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 425 removed outlier: 3.556A pdb=" N GLY d 420 " --> pdb=" O GLN d 417 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE d 421 " --> pdb=" O ILE d 418 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN d 425 " --> pdb=" O PHE d 422 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 11 Processing helix chain 'c' and resid 19 through 22 No H-bonds generated for 'chain 'c' and resid 19 through 22' Processing helix chain 'c' and resid 30 through 43 removed outlier: 3.898A pdb=" N ASP c 35 " --> pdb=" O LEU c 31 " (cutoff:3.500A) Proline residue: c 36 - end of helix removed outlier: 4.101A pdb=" N LEU c 41 " --> pdb=" O ILE c 37 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU c 42 " --> pdb=" O CYS c 38 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE c 43 " --> pdb=" O LYS c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 177 through 184 removed outlier: 4.335A pdb=" N PHE c 181 " --> pdb=" O PHE c 177 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 194 Processing helix chain 'c' and resid 205 through 209 Processing helix chain 'c' and resid 234 through 238 Processing helix chain 'c' and resid 240 through 252 removed outlier: 3.972A pdb=" N ILE c 245 " --> pdb=" O ASN c 241 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE c 246 " --> pdb=" O ASN c 242 " (cutoff:3.500A) Processing helix chain 'c' and resid 259 through 262 No H-bonds generated for 'chain 'c' and resid 259 through 262' Processing helix chain 'c' and resid 265 through 276 removed outlier: 3.866A pdb=" N LYS c 271 " --> pdb=" O TYR c 267 " (cutoff:3.500A) Processing helix chain 'c' and resid 283 through 295 removed outlier: 3.699A pdb=" N GLY c 287 " --> pdb=" O LYS c 283 " (cutoff:3.500A) Processing helix chain 'c' and resid 300 through 305 Processing helix chain 'c' and resid 310 through 312 No H-bonds generated for 'chain 'c' and resid 310 through 312' Processing helix chain 'c' and resid 316 through 325 Processing helix chain 'c' and resid 327 through 332 Processing helix chain 'c' and resid 338 through 340 No H-bonds generated for 'chain 'c' and resid 338 through 340' Processing helix chain 'c' and resid 351 through 365 removed outlier: 3.629A pdb=" N ARG c 363 " --> pdb=" O LYS c 359 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL c 364 " --> pdb=" O GLY c 360 " (cutoff:3.500A) Processing helix chain 'c' and resid 372 through 381 removed outlier: 3.654A pdb=" N PHE c 380 " --> pdb=" O ILE c 376 " (cutoff:3.500A) Processing helix chain 'c' and resid 387 through 394 Processing helix chain 'D' and resid 7 through 11 Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.561A pdb=" N ILE D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 77 removed outlier: 3.558A pdb=" N ILE D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D 73 " --> pdb=" O GLY D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 100 through 110 removed outlier: 3.554A pdb=" N GLN D 103 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 106 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR D 107 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 110 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 141 removed outlier: 3.728A pdb=" N SER D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER D 128 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP D 136 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 137 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 removed outlier: 3.559A pdb=" N ILE D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 164 removed outlier: 3.725A pdb=" N GLU D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 196 removed outlier: 3.924A pdb=" N GLU D 180 " --> pdb=" O PHE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 220 removed outlier: 3.569A pdb=" N GLY D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 220 " --> pdb=" O PHE D 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 213 through 220' Processing helix chain 'D' and resid 248 through 270 removed outlier: 3.556A pdb=" N ILE D 253 " --> pdb=" O ARG D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 282 removed outlier: 3.837A pdb=" N LYS D 278 " --> pdb=" O TYR D 274 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 347 through 349 No H-bonds generated for 'chain 'D' and resid 347 through 349' Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 374 through 394 removed outlier: 3.662A pdb=" N VAL D 378 " --> pdb=" O GLY D 374 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) Proline residue: D 384 - end of helix removed outlier: 4.312A pdb=" N LYS D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 471 through 477 removed outlier: 3.602A pdb=" N LYS D 475 " --> pdb=" O LYS D 471 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 524 removed outlier: 3.587A pdb=" N ILE D 519 " --> pdb=" O PRO D 515 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 520 " --> pdb=" O LEU D 516 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 523 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 524 " --> pdb=" O LYS D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 548 removed outlier: 3.986A pdb=" N ASN D 539 " --> pdb=" O ASN D 535 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU D 547 " --> pdb=" O TYR D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 564 removed outlier: 3.570A pdb=" N LEU D 559 " --> pdb=" O VAL D 555 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE D 560 " --> pdb=" O HIS D 556 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.673A pdb=" N ASN D 592 " --> pdb=" O ILE D 588 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 588 through 593' Processing helix chain 'D' and resid 599 through 602 No H-bonds generated for 'chain 'D' and resid 599 through 602' Processing helix chain 'D' and resid 607 through 612 Processing helix chain 'D' and resid 618 through 620 No H-bonds generated for 'chain 'D' and resid 618 through 620' Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 33 through 44 removed outlier: 3.903A pdb=" N MET C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 128 through 131 No H-bonds generated for 'chain 'C' and resid 128 through 131' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 276 through 279 No H-bonds generated for 'chain 'C' and resid 276 through 279' Processing helix chain 'C' and resid 287 through 305 removed outlier: 3.561A pdb=" N ASN C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 310 No H-bonds generated for 'chain 'C' and resid 307 through 310' Processing helix chain 'C' and resid 319 through 331 removed outlier: 4.033A pdb=" N ARG C 331 " --> pdb=" O ASN C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 434 Processing helix chain 'C' and resid 438 through 451 removed outlier: 4.542A pdb=" N VAL C 442 " --> pdb=" O ASN C 438 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 451 " --> pdb=" O ASP C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 466 removed outlier: 4.494A pdb=" N GLU C 458 " --> pdb=" O LYS C 454 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU C 459 " --> pdb=" O GLU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 481 Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 536 through 538 No H-bonds generated for 'chain 'C' and resid 536 through 538' Processing helix chain 'C' and resid 560 through 562 No H-bonds generated for 'chain 'C' and resid 560 through 562' Processing helix chain 'C' and resid 576 through 584 removed outlier: 4.136A pdb=" N SER C 580 " --> pdb=" O ASN C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 602 through 613 Processing helix chain 'C' and resid 630 through 642 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 Processing sheet with id= B, first strand: chain 'd' and resid 58 through 61 Processing sheet with id= C, first strand: chain 'd' and resid 249 through 252 removed outlier: 3.851A pdb=" N ASN d 377 " --> pdb=" O ASN d 330 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE d 327 " --> pdb=" O LEU d 343 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'd' and resid 254 through 256 removed outlier: 5.818A pdb=" N LEU d 357 " --> pdb=" O THR d 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'd' and resid 265 through 267 removed outlier: 8.097A pdb=" N MET d 267 " --> pdb=" O GLY d 346 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE d 348 " --> pdb=" O MET d 267 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'c' and resid 47 through 49 removed outlier: 3.511A pdb=" N THR c 48 " --> pdb=" O LEU c 85 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'c' and resid 52 through 54 Processing sheet with id= H, first strand: chain 'c' and resid 109 through 112 Processing sheet with id= I, first strand: chain 'c' and resid 122 through 125 Processing sheet with id= J, first strand: chain 'c' and resid 129 through 131 Processing sheet with id= K, first strand: chain 'c' and resid 200 through 203 Processing sheet with id= L, first strand: chain 'D' and resid 4 through 6 removed outlier: 9.725A pdb=" N TYR D 5 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP D 56 " --> pdb=" O TYR D 5 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 302 through 305 removed outlier: 3.533A pdb=" N LEU D 302 " --> pdb=" O ILE D 344 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 488 through 491 removed outlier: 3.543A pdb=" N ILE D 430 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR D 451 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS D 432 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N THR D 449 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 565 through 567 Processing sheet with id= P, first strand: chain 'C' and resid 105 through 110 removed outlier: 3.660A pdb=" N TYR C 93 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLN C 98 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL C 82 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 524 through 529 removed outlier: 6.289A pdb=" N ILE C 400 " --> pdb=" O ALA C 165 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 189 through 196 removed outlier: 3.546A pdb=" N ASP C 267 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 355 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE C 265 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 232 through 234 removed outlier: 3.936A pdb=" N ALA C 232 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 234 " --> pdb=" O THR C 257 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 73 through 75 removed outlier: 3.614A pdb=" N ARG C 74 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR C 145 " --> pdb=" O ARG C 74 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 178 through 181 removed outlier: 7.971A pdb=" N ILE C 180 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE C 379 " --> pdb=" O ILE C 180 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1761 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: 5.69 Time building geometry restraints manager: 9.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7038 1.34 - 1.46: 4871 1.46 - 1.58: 10103 1.58 - 1.70: 5 1.70 - 1.82: 140 Bond restraints: 22157 Sorted by residual: bond pdb=" C3' DU A 502 " pdb=" C4' DU A 502 " ideal model delta sigma weight residual 1.289 1.526 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C3' DU A 503 " pdb=" C4' DU A 503 " ideal model delta sigma weight residual 1.289 1.522 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1' DU A 503 " pdb=" C2' DU A 503 " ideal model delta sigma weight residual 1.316 1.530 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C1' DU A 502 " pdb=" C2' DU A 502 " ideal model delta sigma weight residual 1.316 1.521 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C5 DU A 502 " pdb=" C6 DU A 502 " ideal model delta sigma weight residual 1.486 1.341 0.145 2.00e-02 2.50e+03 5.23e+01 ... (remaining 22152 not shown) Histogram of bond angle deviations from ideal: 96.67 - 104.14: 211 104.14 - 111.61: 9855 111.61 - 119.08: 8104 119.08 - 126.55: 11569 126.55 - 134.02: 143 Bond angle restraints: 29882 Sorted by residual: angle pdb=" CB MET A 219 " pdb=" CG MET A 219 " pdb=" SD MET A 219 " ideal model delta sigma weight residual 112.70 121.82 -9.12 3.00e+00 1.11e-01 9.24e+00 angle pdb=" C ILE A 375 " pdb=" N ILE A 376 " pdb=" CA ILE A 376 " ideal model delta sigma weight residual 120.33 122.73 -2.40 8.00e-01 1.56e+00 9.03e+00 angle pdb=" C GLU C 175 " pdb=" CA GLU C 175 " pdb=" CB GLU C 175 " ideal model delta sigma weight residual 110.42 116.00 -5.58 1.99e+00 2.53e-01 7.86e+00 angle pdb=" CB MET C 154 " pdb=" CG MET C 154 " pdb=" SD MET C 154 " ideal model delta sigma weight residual 112.70 121.07 -8.37 3.00e+00 1.11e-01 7.78e+00 angle pdb=" CB MET C 460 " pdb=" CG MET C 460 " pdb=" SD MET C 460 " ideal model delta sigma weight residual 112.70 120.56 -7.86 3.00e+00 1.11e-01 6.87e+00 ... (remaining 29877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 11910 17.22 - 34.45: 1283 34.45 - 51.67: 285 51.67 - 68.90: 35 68.90 - 86.12: 9 Dihedral angle restraints: 13522 sinusoidal: 5680 harmonic: 7842 Sorted by residual: dihedral pdb=" CA PHE A 156 " pdb=" C PHE A 156 " pdb=" N ASN A 157 " pdb=" CA ASN A 157 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLN c 284 " pdb=" C GLN c 284 " pdb=" N GLU c 285 " pdb=" CA GLU c 285 " ideal model delta harmonic sigma weight residual 180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASN C 208 " pdb=" CB ASN C 208 " pdb=" CG ASN C 208 " pdb=" OD1 ASN C 208 " ideal model delta sinusoidal sigma weight residual -90.00 -164.23 74.23 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 13519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3079 0.074 - 0.148: 245 0.148 - 0.222: 2 0.222 - 0.296: 0 0.296 - 0.369: 1 Chirality restraints: 3327 Sorted by residual: chirality pdb=" C3' DU A 502 " pdb=" C2' DU A 502 " pdb=" C4' DU A 502 " pdb=" O3' DU A 502 " both_signs ideal model delta sigma weight residual False -2.42 -2.79 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C3' DU A 503 " pdb=" C2' DU A 503 " pdb=" C4' DU A 503 " pdb=" O3' DU A 503 " both_signs ideal model delta sigma weight residual False -2.42 -2.61 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" C1' DU A 502 " pdb=" C2' DU A 502 " pdb=" N1 DU A 502 " pdb=" O4' DU A 502 " both_signs ideal model delta sigma weight residual False 2.36 2.50 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 3324 not shown) Planarity restraints: 3830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 234 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 235 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 262 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" CG ASP C 262 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP C 262 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP C 262 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS c 438 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO c 439 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO c 439 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO c 439 " 0.021 5.00e-02 4.00e+02 ... (remaining 3827 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3637 2.76 - 3.29: 21106 3.29 - 3.83: 33379 3.83 - 4.36: 37715 4.36 - 4.90: 64822 Nonbonded interactions: 160659 Sorted by model distance: nonbonded pdb=" OD2 ASP c 106 " pdb=" OH TYR c 109 " model vdw 2.224 2.440 nonbonded pdb=" O LYS A 238 " pdb=" OG SER A 241 " model vdw 2.231 2.440 nonbonded pdb=" NH2 ARG A 292 " pdb=" O TYR d 45 " model vdw 2.233 2.520 nonbonded pdb=" O ASP D 521 " pdb=" OG1 THR D 525 " model vdw 2.236 2.440 nonbonded pdb=" O ILE A 401 " pdb=" OG SER A 404 " model vdw 2.239 2.440 ... (remaining 160654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 3.230 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 61.500 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.005 0.237 22157 Z= 0.314 Angle : 0.512 9.120 29882 Z= 0.280 Chirality : 0.040 0.369 3327 Planarity : 0.003 0.043 3830 Dihedral : 14.466 86.119 8458 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.12 % Allowed : 19.61 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.49 (0.16), residues: 2637 helix: 0.33 (0.16), residues: 1055 sheet: -0.07 (0.35), residues: 251 loop : -0.86 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 268 HIS 0.003 0.001 HIS C 509 PHE 0.025 0.001 PHE A 156 TYR 0.015 0.001 TYR A 73 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 2.783 Fit side-chains REVERT: d 242 MET cc_start: 0.8867 (tmm) cc_final: 0.8406 (tmm) outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 0.2881 time to fit residues: 49.6609 Evaluate side-chains 95 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 67 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 117 ASN ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 372 ASN A 393 ASN d 24 ASN d 99 ASN d 120 ASN d 158 HIS d 282 ASN c 14 GLN c 24 ASN c 279 ASN c 369 ASN c 474 HIS D 8 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 ASN D 412 ASN D 494 ASN D 551 ASN C 16 HIS C 29 ASN C 50 GLN C 119 HIS C 153 ASN C 203 ASN C 208 ASN C 412 ASN C 415 GLN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22157 Z= 0.384 Angle : 0.571 7.532 29882 Z= 0.301 Chirality : 0.042 0.146 3327 Planarity : 0.003 0.048 3830 Dihedral : 5.166 59.383 2894 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.77 % Allowed : 18.68 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.58 (0.16), residues: 2637 helix: 0.46 (0.16), residues: 1049 sheet: -0.27 (0.36), residues: 231 loop : -1.07 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP c 268 HIS 0.006 0.001 HIS C 16 PHE 0.017 0.002 PHE C 352 TYR 0.016 0.002 TYR C 598 ARG 0.002 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 86 time to evaluate : 2.528 Fit side-chains REVERT: A 237 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7641 (mp) REVERT: A 323 MET cc_start: 0.9094 (mmm) cc_final: 0.8792 (mmm) REVERT: c 41 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9176 (tp) REVERT: c 194 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7463 (m-10) REVERT: D 292 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7278 (p0) REVERT: D 494 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8865 (m110) REVERT: D 627 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8694 (tt) REVERT: C 154 MET cc_start: 0.7185 (tpp) cc_final: 0.6925 (tpp) REVERT: C 412 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8757 (p0) outliers start: 93 outliers final: 51 residues processed: 170 average time/residue: 0.2752 time to fit residues: 80.7450 Evaluate side-chains 142 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 84 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain d residue 106 ILE Chi-restraints excluded: chain d residue 146 ASP Chi-restraints excluded: chain d residue 158 HIS Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 204 ASP Chi-restraints excluded: chain d residue 221 ILE Chi-restraints excluded: chain d residue 237 LEU Chi-restraints excluded: chain d residue 255 THR Chi-restraints excluded: chain d residue 334 THR Chi-restraints excluded: chain d residue 340 ILE Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 177 PHE Chi-restraints excluded: chain c residue 194 PHE Chi-restraints excluded: chain c residue 202 VAL Chi-restraints excluded: chain c residue 204 MET Chi-restraints excluded: chain c residue 252 CYS Chi-restraints excluded: chain c residue 290 ILE Chi-restraints excluded: chain c residue 312 ASN Chi-restraints excluded: chain c residue 316 ILE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 494 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 567 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 237 optimal weight: 0.9990 chunk 256 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN c 351 HIS ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 488 GLN C 412 ASN C 438 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22157 Z= 0.143 Angle : 0.430 7.515 29882 Z= 0.228 Chirality : 0.039 0.152 3327 Planarity : 0.003 0.047 3830 Dihedral : 4.782 58.620 2892 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.47 % Allowed : 20.06 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.29 (0.16), residues: 2637 helix: 0.75 (0.16), residues: 1065 sheet: -0.23 (0.35), residues: 242 loop : -0.94 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 59 HIS 0.005 0.001 HIS d 158 PHE 0.010 0.001 PHE C 352 TYR 0.012 0.001 TYR C 512 ARG 0.002 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 92 time to evaluate : 2.513 Fit side-chains REVERT: A 75 MET cc_start: 0.8620 (mmt) cc_final: 0.8416 (ppp) REVERT: A 323 MET cc_start: 0.9060 (mmm) cc_final: 0.8844 (mmm) REVERT: c 194 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: c 223 MET cc_start: 0.7828 (ppp) cc_final: 0.7613 (tmm) REVERT: C 126 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8848 (p0) REVERT: C 154 MET cc_start: 0.7049 (tpp) cc_final: 0.6833 (tpp) REVERT: C 412 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8210 (p0) outliers start: 61 outliers final: 27 residues processed: 144 average time/residue: 0.2598 time to fit residues: 64.7286 Evaluate side-chains 117 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain d residue 146 ASP Chi-restraints excluded: chain d residue 204 ASP Chi-restraints excluded: chain d residue 253 VAL Chi-restraints excluded: chain d residue 334 THR Chi-restraints excluded: chain d residue 340 ILE Chi-restraints excluded: chain c residue 177 PHE Chi-restraints excluded: chain c residue 194 PHE Chi-restraints excluded: chain c residue 204 MET Chi-restraints excluded: chain c residue 217 ASN Chi-restraints excluded: chain c residue 312 ASN Chi-restraints excluded: chain c residue 316 ILE Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 567 TYR Chi-restraints excluded: chain C residue 577 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 0.0980 chunk 178 optimal weight: 0.1980 chunk 123 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 238 optimal weight: 0.2980 chunk 252 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 158 HIS c 239 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22157 Z= 0.125 Angle : 0.417 8.770 29882 Z= 0.218 Chirality : 0.039 0.146 3327 Planarity : 0.002 0.046 3830 Dihedral : 4.616 59.163 2892 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.47 % Allowed : 20.18 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.16 (0.16), residues: 2637 helix: 0.87 (0.17), residues: 1059 sheet: -0.18 (0.35), residues: 242 loop : -0.87 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP c 268 HIS 0.002 0.000 HIS C 509 PHE 0.010 0.001 PHE c 276 TYR 0.011 0.001 TYR C 512 ARG 0.001 0.000 ARG d 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 93 time to evaluate : 2.705 Fit side-chains REVERT: A 307 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8749 (tm-30) REVERT: A 323 MET cc_start: 0.9061 (mmm) cc_final: 0.8810 (mmm) REVERT: c 41 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9137 (tp) REVERT: c 194 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7639 (m-10) REVERT: c 223 MET cc_start: 0.7875 (ppp) cc_final: 0.7560 (tmm) REVERT: C 22 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: C 154 MET cc_start: 0.7076 (tpp) cc_final: 0.6786 (tpp) outliers start: 61 outliers final: 36 residues processed: 143 average time/residue: 0.2705 time to fit residues: 67.2693 Evaluate side-chains 129 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 90 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 146 ASP Chi-restraints excluded: chain d residue 204 ASP Chi-restraints excluded: chain d residue 253 VAL Chi-restraints excluded: chain d residue 334 THR Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 194 PHE Chi-restraints excluded: chain c residue 202 VAL Chi-restraints excluded: chain c residue 204 MET Chi-restraints excluded: chain c residue 252 CYS Chi-restraints excluded: chain c residue 316 ILE Chi-restraints excluded: chain c residue 447 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 567 TYR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 620 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 174 optimal weight: 0.0270 chunk 0 optimal weight: 60.0000 chunk 128 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22157 Z= 0.183 Angle : 0.432 8.259 29882 Z= 0.227 Chirality : 0.039 0.148 3327 Planarity : 0.002 0.045 3830 Dihedral : 4.623 54.773 2892 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.88 % Allowed : 19.69 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.19 (0.16), residues: 2637 helix: 0.86 (0.17), residues: 1059 sheet: -0.18 (0.35), residues: 242 loop : -0.91 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP c 268 HIS 0.008 0.001 HIS d 158 PHE 0.012 0.001 PHE c 5 TYR 0.013 0.001 TYR C 512 ARG 0.004 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 91 time to evaluate : 2.627 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8620 (mmt) cc_final: 0.8378 (ppp) REVERT: A 307 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8740 (tm-30) REVERT: A 323 MET cc_start: 0.9078 (mmm) cc_final: 0.8812 (mmm) REVERT: d 364 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8875 (tp) REVERT: c 194 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7485 (m-10) REVERT: c 223 MET cc_start: 0.7872 (ppp) cc_final: 0.7567 (tmm) REVERT: D 411 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: C 22 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: C 412 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8161 (p0) outliers start: 71 outliers final: 51 residues processed: 151 average time/residue: 0.3016 time to fit residues: 78.9917 Evaluate side-chains 145 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 89 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 146 ASP Chi-restraints excluded: chain d residue 204 ASP Chi-restraints excluded: chain d residue 253 VAL Chi-restraints excluded: chain d residue 334 THR Chi-restraints excluded: chain d residue 340 ILE Chi-restraints excluded: chain d residue 364 LEU Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 177 PHE Chi-restraints excluded: chain c residue 194 PHE Chi-restraints excluded: chain c residue 202 VAL Chi-restraints excluded: chain c residue 204 MET Chi-restraints excluded: chain c residue 217 ASN Chi-restraints excluded: chain c residue 252 CYS Chi-restraints excluded: chain c residue 312 ASN Chi-restraints excluded: chain c residue 316 ILE Chi-restraints excluded: chain c residue 447 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 567 TYR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 620 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 0.0570 chunk 227 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 83 optimal weight: 0.2980 chunk 132 optimal weight: 9.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22157 Z= 0.113 Angle : 0.419 11.328 29882 Z= 0.215 Chirality : 0.039 0.232 3327 Planarity : 0.002 0.045 3830 Dihedral : 4.472 54.373 2892 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.59 % Allowed : 20.14 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2637 helix: 0.98 (0.17), residues: 1058 sheet: -0.06 (0.35), residues: 242 loop : -0.86 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 423 HIS 0.002 0.000 HIS d 158 PHE 0.008 0.001 PHE D 489 TYR 0.010 0.001 TYR A 61 ARG 0.003 0.000 ARG C 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 94 time to evaluate : 3.030 Fit side-chains REVERT: A 307 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8684 (tm-30) REVERT: A 323 MET cc_start: 0.9090 (mmm) cc_final: 0.8843 (mmm) REVERT: c 194 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7608 (m-10) REVERT: c 223 MET cc_start: 0.7894 (ppp) cc_final: 0.7585 (tmm) REVERT: D 246 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8140 (mp) REVERT: D 411 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: D 521 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8212 (t70) REVERT: C 22 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: C 154 MET cc_start: 0.7647 (mmm) cc_final: 0.7056 (tpp) outliers start: 64 outliers final: 47 residues processed: 147 average time/residue: 0.2722 time to fit residues: 69.4423 Evaluate side-chains 143 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 91 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 146 ASP Chi-restraints excluded: chain d residue 204 ASP Chi-restraints excluded: chain d residue 253 VAL Chi-restraints excluded: chain d residue 334 THR Chi-restraints excluded: chain d residue 386 MET Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 177 PHE Chi-restraints excluded: chain c residue 194 PHE Chi-restraints excluded: chain c residue 202 VAL Chi-restraints excluded: chain c residue 204 MET Chi-restraints excluded: chain c residue 217 ASN Chi-restraints excluded: chain c residue 268 TRP Chi-restraints excluded: chain c residue 316 ILE Chi-restraints excluded: chain c residue 362 TYR Chi-restraints excluded: chain c residue 447 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 567 TYR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 620 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 10.0000 chunk 28 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 HIS ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22157 Z= 0.272 Angle : 0.499 11.893 29882 Z= 0.257 Chirality : 0.041 0.225 3327 Planarity : 0.003 0.044 3830 Dihedral : 4.821 54.703 2892 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.12 % Allowed : 20.10 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.23 (0.16), residues: 2637 helix: 0.90 (0.17), residues: 1039 sheet: -0.18 (0.35), residues: 232 loop : -0.97 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP c 268 HIS 0.004 0.001 HIS C 506 PHE 0.025 0.001 PHE A 156 TYR 0.024 0.001 TYR A 87 ARG 0.002 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 87 time to evaluate : 2.843 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 323 MET cc_start: 0.9107 (mmm) cc_final: 0.8828 (mmm) REVERT: d 364 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8848 (tp) REVERT: c 194 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: D 246 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8131 (mp) REVERT: D 411 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: D 477 LEU cc_start: 0.7936 (tp) cc_final: 0.7694 (tt) REVERT: D 521 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8103 (t0) REVERT: C 22 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: C 193 VAL cc_start: 0.9573 (OUTLIER) cc_final: 0.9323 (t) REVERT: C 592 MET cc_start: 0.8232 (tpp) cc_final: 0.7959 (tpp) outliers start: 77 outliers final: 60 residues processed: 153 average time/residue: 0.2870 time to fit residues: 75.1295 Evaluate side-chains 153 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 86 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 146 ASP Chi-restraints excluded: chain d residue 204 ASP Chi-restraints excluded: chain d residue 253 VAL Chi-restraints excluded: chain d residue 334 THR Chi-restraints excluded: chain d residue 364 LEU Chi-restraints excluded: chain d residue 386 MET Chi-restraints excluded: chain d residue 410 ASP Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 177 PHE Chi-restraints excluded: chain c residue 194 PHE Chi-restraints excluded: chain c residue 202 VAL Chi-restraints excluded: chain c residue 204 MET Chi-restraints excluded: chain c residue 217 ASN Chi-restraints excluded: chain c residue 252 CYS Chi-restraints excluded: chain c residue 268 TRP Chi-restraints excluded: chain c residue 312 ASN Chi-restraints excluded: chain c residue 316 ILE Chi-restraints excluded: chain c residue 447 LEU Chi-restraints excluded: chain c residue 481 ILE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 567 TYR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 640 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 0.0970 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22157 Z= 0.248 Angle : 0.488 12.940 29882 Z= 0.251 Chirality : 0.040 0.263 3327 Planarity : 0.003 0.044 3830 Dihedral : 4.893 57.786 2892 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.24 % Allowed : 20.26 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.32 (0.16), residues: 2637 helix: 0.84 (0.16), residues: 1053 sheet: -0.22 (0.35), residues: 232 loop : -1.06 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP c 268 HIS 0.004 0.001 HIS C 506 PHE 0.020 0.001 PHE A 156 TYR 0.020 0.001 TYR A 87 ARG 0.002 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 87 time to evaluate : 2.999 Fit side-chains REVERT: A 33 MET cc_start: 0.6661 (pmm) cc_final: 0.6252 (pmm) REVERT: A 307 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8741 (tm-30) REVERT: A 323 MET cc_start: 0.9112 (mmm) cc_final: 0.8821 (mmm) REVERT: d 242 MET cc_start: 0.8848 (tmm) cc_final: 0.8628 (ttp) REVERT: d 364 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8845 (tp) REVERT: c 194 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7525 (m-10) REVERT: D 246 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8128 (mp) REVERT: D 411 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: D 477 LEU cc_start: 0.7985 (tp) cc_final: 0.7743 (tt) REVERT: D 521 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8084 (t0) REVERT: C 22 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: C 154 MET cc_start: 0.7751 (mmm) cc_final: 0.7182 (tpp) outliers start: 80 outliers final: 61 residues processed: 157 average time/residue: 0.2689 time to fit residues: 73.4329 Evaluate side-chains 152 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 85 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 146 ASP Chi-restraints excluded: chain d residue 176 PHE Chi-restraints excluded: chain d residue 204 ASP Chi-restraints excluded: chain d residue 253 VAL Chi-restraints excluded: chain d residue 334 THR Chi-restraints excluded: chain d residue 364 LEU Chi-restraints excluded: chain d residue 386 MET Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 177 PHE Chi-restraints excluded: chain c residue 194 PHE Chi-restraints excluded: chain c residue 202 VAL Chi-restraints excluded: chain c residue 204 MET Chi-restraints excluded: chain c residue 217 ASN Chi-restraints excluded: chain c residue 252 CYS Chi-restraints excluded: chain c residue 312 ASN Chi-restraints excluded: chain c residue 316 ILE Chi-restraints excluded: chain c residue 320 VAL Chi-restraints excluded: chain c residue 447 LEU Chi-restraints excluded: chain c residue 481 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 567 TYR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 640 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 184 optimal weight: 0.0870 chunk 71 optimal weight: 0.0980 chunk 211 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22157 Z= 0.119 Angle : 0.440 14.062 29882 Z= 0.223 Chirality : 0.039 0.273 3327 Planarity : 0.002 0.045 3830 Dihedral : 4.621 58.188 2892 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.67 % Allowed : 20.91 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.13 (0.16), residues: 2637 helix: 1.00 (0.17), residues: 1056 sheet: -0.28 (0.34), residues: 250 loop : -0.92 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 59 HIS 0.003 0.001 HIS d 158 PHE 0.017 0.001 PHE A 156 TYR 0.016 0.001 TYR A 87 ARG 0.001 0.000 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 89 time to evaluate : 2.664 Fit side-chains REVERT: A 33 MET cc_start: 0.6608 (pmm) cc_final: 0.6220 (pmm) REVERT: A 307 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8675 (tm-30) REVERT: A 323 MET cc_start: 0.9090 (mmm) cc_final: 0.8803 (mmm) REVERT: d 242 MET cc_start: 0.8829 (tmm) cc_final: 0.8592 (ttp) REVERT: d 364 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8925 (tp) REVERT: D 246 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8128 (mp) REVERT: D 477 LEU cc_start: 0.7971 (tp) cc_final: 0.7751 (tt) REVERT: D 521 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8021 (t0) REVERT: C 22 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: C 154 MET cc_start: 0.7649 (mmm) cc_final: 0.7101 (tpp) REVERT: C 193 VAL cc_start: 0.9577 (OUTLIER) cc_final: 0.9333 (t) REVERT: C 328 CYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8235 (t) outliers start: 66 outliers final: 51 residues processed: 146 average time/residue: 0.2660 time to fit residues: 67.5715 Evaluate side-chains 147 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 90 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 146 ASP Chi-restraints excluded: chain d residue 204 ASP Chi-restraints excluded: chain d residue 253 VAL Chi-restraints excluded: chain d residue 334 THR Chi-restraints excluded: chain d residue 340 ILE Chi-restraints excluded: chain d residue 364 LEU Chi-restraints excluded: chain d residue 410 ASP Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 177 PHE Chi-restraints excluded: chain c residue 202 VAL Chi-restraints excluded: chain c residue 204 MET Chi-restraints excluded: chain c residue 217 ASN Chi-restraints excluded: chain c residue 252 CYS Chi-restraints excluded: chain c residue 268 TRP Chi-restraints excluded: chain c residue 320 VAL Chi-restraints excluded: chain c residue 447 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 567 TYR Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 640 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 260 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 207 optimal weight: 0.0030 chunk 21 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22157 Z= 0.155 Angle : 0.451 14.098 29882 Z= 0.227 Chirality : 0.039 0.280 3327 Planarity : 0.002 0.044 3830 Dihedral : 4.590 58.328 2892 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.39 % Allowed : 21.19 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.13 (0.16), residues: 2637 helix: 1.00 (0.17), residues: 1054 sheet: -0.27 (0.34), residues: 250 loop : -0.92 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP c 268 HIS 0.003 0.001 HIS d 158 PHE 0.017 0.001 PHE A 156 TYR 0.016 0.001 TYR A 87 ARG 0.003 0.000 ARG C 573 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5274 Ramachandran restraints generated. 2637 Oldfield, 0 Emsley, 2637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 85 time to evaluate : 2.592 Fit side-chains REVERT: A 33 MET cc_start: 0.6488 (pmm) cc_final: 0.6129 (pmm) REVERT: A 307 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8681 (tm-30) REVERT: A 323 MET cc_start: 0.9096 (mmm) cc_final: 0.8809 (mmm) REVERT: d 242 MET cc_start: 0.8808 (tmm) cc_final: 0.8586 (ttp) REVERT: d 364 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8908 (tp) REVERT: D 246 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8142 (mp) REVERT: D 477 LEU cc_start: 0.7982 (tp) cc_final: 0.7765 (tt) REVERT: D 521 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8066 (t0) REVERT: C 22 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: C 154 MET cc_start: 0.7632 (mmm) cc_final: 0.7087 (tpp) REVERT: C 193 VAL cc_start: 0.9577 (OUTLIER) cc_final: 0.9336 (t) outliers start: 59 outliers final: 50 residues processed: 137 average time/residue: 0.2843 time to fit residues: 67.7499 Evaluate side-chains 139 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 84 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 146 ASP Chi-restraints excluded: chain d residue 204 ASP Chi-restraints excluded: chain d residue 237 LEU Chi-restraints excluded: chain d residue 253 VAL Chi-restraints excluded: chain d residue 334 THR Chi-restraints excluded: chain d residue 340 ILE Chi-restraints excluded: chain d residue 364 LEU Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 177 PHE Chi-restraints excluded: chain c residue 202 VAL Chi-restraints excluded: chain c residue 204 MET Chi-restraints excluded: chain c residue 217 ASN Chi-restraints excluded: chain c residue 252 CYS Chi-restraints excluded: chain c residue 268 TRP Chi-restraints excluded: chain c residue 320 VAL Chi-restraints excluded: chain c residue 447 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 567 TYR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 640 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.083712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063745 restraints weight = 67959.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.065816 restraints weight = 38393.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.067186 restraints weight = 26730.244| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22157 Z= 0.220 Angle : 0.476 13.865 29882 Z= 0.242 Chirality : 0.040 0.269 3327 Planarity : 0.003 0.044 3830 Dihedral : 4.733 58.443 2892 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.88 % Allowed : 20.75 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.20 (0.16), residues: 2637 helix: 0.94 (0.17), residues: 1054 sheet: -0.27 (0.35), residues: 237 loop : -0.98 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP c 268 HIS 0.004 0.001 HIS C 506 PHE 0.016 0.001 PHE A 156 TYR 0.016 0.001 TYR A 87 ARG 0.001 0.000 ARG D 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3084.33 seconds wall clock time: 58 minutes 32.77 seconds (3512.77 seconds total)