Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 02:16:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/04_2023/7um0_24763_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/04_2023/7um0_24763.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/04_2023/7um0_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_24763/04_2023/7um0_24763_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/04_2023/7um0_24763_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/04_2023/7um0_24763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/04_2023/7um0_24763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/04_2023/7um0_24763_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um0_24763/04_2023/7um0_24763_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-1.21rc1-4938/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: 11.47, per 1000 atoms: 0.53 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: 8.14 Conformation dependent library (CDL) restraints added in 2.9 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: 2.34 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: 6.29 Time building geometry restraints manager: 8.72 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: 11902 17.22 - 34.45: 1282 34.45 - 51.67: 284 51.67 - 68.90: 34 68.90 - 86.12: 8 Dihedral angle restraints: 13510 sinusoidal: 5668 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 13507 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 4.040 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 55.310 Find NCS groups from input model: 0.720 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.380 ------------------------------------------------------------------------------- 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 : 14.419 86.119 8446 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 % 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 *********************** 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 : 2.765 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 0.2968 time to fit residues: 51.5374 Evaluate side-chains 95 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 2.773 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1890 time to fit residues: 4.1770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 C 576 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 22157 Z= 0.383 Angle : 0.576 7.674 29882 Z= 0.304 Chirality : 0.043 0.149 3327 Planarity : 0.003 0.049 3830 Dihedral : 5.056 58.356 2880 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 3.77 % 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: -0.62 (0.16), residues: 2637 helix: 0.45 (0.16), residues: 1043 sheet: -0.32 (0.35), residues: 233 loop : -1.09 (0.16), residues: 1361 *********************** 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 : 2.659 Fit side-chains outliers start: 93 outliers final: 50 residues processed: 172 average time/residue: 0.2752 time to fit residues: 81.9386 Evaluate side-chains 132 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 82 time to evaluate : 2.902 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.2176 time to fit residues: 24.3167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 161 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 256 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 351 HIS ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 22157 Z= 0.268 Angle : 0.493 9.357 29882 Z= 0.260 Chirality : 0.041 0.148 3327 Planarity : 0.003 0.049 3830 Dihedral : 4.889 51.740 2880 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 2.19 % 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: -0.51 (0.16), residues: 2637 helix: 0.65 (0.16), residues: 1044 sheet: -0.32 (0.35), residues: 231 loop : -1.13 (0.16), residues: 1362 *********************** 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 139 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 85 time to evaluate : 2.985 Fit side-chains outliers start: 54 outliers final: 24 residues processed: 134 average time/residue: 0.2770 time to fit residues: 65.3685 Evaluate side-chains 108 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 2.685 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1941 time to fit residues: 12.4646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 123 optimal weight: 0.1980 chunk 26 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** c 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN C 415 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 22157 Z= 0.212 Angle : 0.463 8.403 29882 Z= 0.243 Chirality : 0.040 0.149 3327 Planarity : 0.003 0.048 3830 Dihedral : 4.728 50.787 2880 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.82 % 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: -0.41 (0.16), residues: 2637 helix: 0.73 (0.16), residues: 1059 sheet: -0.33 (0.35), residues: 231 loop : -1.08 (0.16), residues: 1347 *********************** 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 135 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 90 time to evaluate : 2.815 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 19 residues processed: 129 average time/residue: 0.2793 time to fit residues: 63.3614 Evaluate side-chains 105 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 2.621 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1956 time to fit residues: 10.6526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 0 optimal weight: 60.0000 chunk 128 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 22157 Z= 0.294 Angle : 0.516 8.415 29882 Z= 0.270 Chirality : 0.041 0.144 3327 Planarity : 0.003 0.048 3830 Dihedral : 4.895 55.991 2880 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.50 % 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: -0.53 (0.16), residues: 2637 helix: 0.68 (0.16), residues: 1044 sheet: -0.39 (0.35), residues: 228 loop : -1.17 (0.16), residues: 1365 *********************** 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 125 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 88 time to evaluate : 2.722 Fit side-chains outliers start: 37 outliers final: 17 residues processed: 124 average time/residue: 0.3001 time to fit residues: 63.9809 Evaluate side-chains 102 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 2.658 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1974 time to fit residues: 10.2097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 7.9990 chunk 227 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 22157 Z= 0.366 Angle : 0.570 9.477 29882 Z= 0.296 Chirality : 0.042 0.175 3327 Planarity : 0.003 0.048 3830 Dihedral : 5.163 57.215 2880 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 1.86 % 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: -0.76 (0.16), residues: 2637 helix: 0.54 (0.16), residues: 1032 sheet: -0.50 (0.35), residues: 223 loop : -1.33 (0.16), residues: 1382 *********************** 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 129 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 83 time to evaluate : 2.987 Fit side-chains outliers start: 46 outliers final: 23 residues processed: 125 average time/residue: 0.3057 time to fit residues: 66.0784 Evaluate side-chains 105 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 2.837 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2109 time to fit residues: 12.7657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 143 optimal weight: 8.9990 chunk 184 optimal weight: 0.1980 chunk 142 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 157 optimal weight: 0.0270 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- 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 488 GLN C 412 ASN C 415 GLN ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 22157 Z= 0.116 Angle : 0.447 11.727 29882 Z= 0.232 Chirality : 0.039 0.204 3327 Planarity : 0.003 0.049 3830 Dihedral : 4.645 57.500 2880 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 0.61 % 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: -0.40 (0.16), residues: 2637 helix: 0.79 (0.17), residues: 1054 sheet: -0.50 (0.35), residues: 223 loop : -1.07 (0.16), residues: 1360 *********************** 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 103 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 2.787 Fit side-chains outliers start: 15 outliers final: 1 residues processed: 100 average time/residue: 0.3018 time to fit residues: 52.8562 Evaluate side-chains 86 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2009 time to fit residues: 4.4533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 75 optimal weight: 0.0980 chunk 49 optimal weight: 0.0020 chunk 48 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 overall best weight: 3.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 239 ASN D 138 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 22157 Z= 0.186 Angle : 0.479 12.687 29882 Z= 0.243 Chirality : 0.040 0.254 3327 Planarity : 0.003 0.047 3830 Dihedral : 4.590 57.829 2880 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.49 % 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: -0.37 (0.16), residues: 2637 helix: 0.84 (0.17), residues: 1053 sheet: -0.43 (0.35), residues: 228 loop : -1.08 (0.16), residues: 1356 *********************** 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 96 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 3.281 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 94 average time/residue: 0.3155 time to fit residues: 53.1619 Evaluate side-chains 88 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 2.756 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2238 time to fit residues: 5.5490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 chunk 219 optimal weight: 0.5980 chunk 234 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 184 optimal weight: 0.7980 chunk 71 optimal weight: 0.0970 chunk 211 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 overall best weight: 2.2982 ------------------------------------------------------------------------------- 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** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 22157 Z= 0.152 Angle : 0.461 13.470 29882 Z= 0.234 Chirality : 0.040 0.274 3327 Planarity : 0.003 0.047 3830 Dihedral : 4.501 57.851 2880 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.28 % 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: -0.34 (0.16), residues: 2637 helix: 0.87 (0.17), residues: 1054 sheet: -0.46 (0.34), residues: 241 loop : -1.07 (0.16), residues: 1342 *********************** 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 92 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 2.700 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 91 average time/residue: 0.3040 time to fit residues: 48.7030 Evaluate side-chains 88 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2188 time to fit residues: 4.4379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 260 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** 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: 0.8298 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 22157 Z= 0.136 Angle : 0.464 13.855 29882 Z= 0.233 Chirality : 0.039 0.282 3327 Planarity : 0.002 0.047 3830 Dihedral : 4.402 58.050 2880 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.24 % 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: -0.28 (0.16), residues: 2637 helix: 0.93 (0.17), residues: 1056 sheet: -0.44 (0.34), residues: 242 loop : -1.04 (0.16), residues: 1339 ********************** 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 94 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 3.086 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 91 average time/residue: 0.3126 time to fit residues: 50.4946 Evaluate side-chains 89 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 2.993 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2798 time to fit residues: 5.3779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 0.0980 chunk 164 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 86 optimal weight: 0.0070 chunk 212 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 overall best weight: 2.2202 ------------------------------------------------------------------------------- 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** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.085621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.064566 restraints weight = 69832.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.066747 restraints weight = 38688.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.068207 restraints weight = 26654.185| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 22157 Z= 0.151 Angle : 0.462 13.652 29882 Z= 0.233 Chirality : 0.039 0.280 3327 Planarity : 0.002 0.046 3830 Dihedral : 4.374 58.225 2880 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.20 % 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: -0.22 (0.16), residues: 2637 helix: 0.97 (0.17), residues: 1050 sheet: -0.43 (0.34), residues: 242 loop : -0.99 (0.16), residues: 1345 =============================================================================== Job complete usr+sys time: 2826.15 seconds wall clock time: 53 minutes 54.29 seconds (3234.29 seconds total)