Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 10:27:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/04_2023/7c4j_30285.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/04_2023/7c4j_30285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/04_2023/7c4j_30285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/04_2023/7c4j_30285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/04_2023/7c4j_30285.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/04_2023/7c4j_30285.pdb" } resolution = 2.89 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 19026 2.51 5 N 5085 2.21 5 O 5570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 58": "OD1" <-> "OD2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 510": "OD1" <-> "OD2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A ASP 532": "OD1" <-> "OD2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B ASP 524": "OD1" <-> "OD2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ASP 545": "OD1" <-> "OD2" Residue "B ARG 564": "NH1" <-> "NH2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 667": "NH1" <-> "NH2" Residue "B PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 711": "OE1" <-> "OE2" Residue "B GLU 720": "OE1" <-> "OE2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B ASP 768": "OD1" <-> "OD2" Residue "B PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D GLU 530": "OE1" <-> "OE2" Residue "D PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 559": "OE1" <-> "OE2" Residue "D ASP 578": "OD1" <-> "OD2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 635": "OE1" <-> "OE2" Residue "D GLU 651": "OE1" <-> "OE2" Residue "D TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 667": "NH1" <-> "NH2" Residue "D PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 688": "NH1" <-> "NH2" Residue "D PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 762": "OE1" <-> "OE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E ARG 205": "NH1" <-> "NH2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 319": "NH1" <-> "NH2" Residue "E ARG 322": "NH1" <-> "NH2" Residue "E TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 522": "OD1" <-> "OD2" Residue "E PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 376": "NH1" <-> "NH2" Residue "F TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "F TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 465": "OD1" <-> "OD2" Residue "F ASP 467": "OD1" <-> "OD2" Residue "F ASP 469": "OD1" <-> "OD2" Residue "F PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 493": "OD1" <-> "OD2" Residue "F ASP 494": "OD1" <-> "OD2" Residue "F ARG 506": "NH1" <-> "NH2" Residue "F ASP 511": "OD1" <-> "OD2" Residue "F GLU 523": "OE1" <-> "OE2" Residue "F ASP 535": "OD1" <-> "OD2" Residue "F ARG 536": "NH1" <-> "NH2" Residue "F ASP 549": "OD1" <-> "OD2" Residue "F PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F ASP 569": "OD1" <-> "OD2" Residue "F PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 621": "OE1" <-> "OE2" Residue "F ASP 623": "OD1" <-> "OD2" Residue "F ARG 640": "NH1" <-> "NH2" Residue "F PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 662": "NH1" <-> "NH2" Residue "F ASP 664": "OD1" <-> "OD2" Residue "F ASP 722": "OD1" <-> "OD2" Residue "F ASP 725": "OD1" <-> "OD2" Residue "F GLU 750": "OE1" <-> "OE2" Residue "H ASP 432": "OD1" <-> "OD2" Residue "H ASP 444": "OD1" <-> "OD2" Residue "H ASP 445": "OD1" <-> "OD2" Residue "H TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 473": "OD1" <-> "OD2" Residue "H PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 520": "OE1" <-> "OE2" Residue "H TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 595": "OE1" <-> "OE2" Residue "I TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 772": "NH1" <-> "NH2" Residue "I ASP 793": "OD1" <-> "OD2" Residue "I ASP 797": "OD1" <-> "OD2" Residue "I ARG 869": "NH1" <-> "NH2" Residue "I PHE 875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 881": "NH1" <-> "NH2" Residue "I GLU 894": "OE1" <-> "OE2" Residue "I PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 936": "NH1" <-> "NH2" Residue "I ARG 940": "NH1" <-> "NH2" Residue "I PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 966": "NH1" <-> "NH2" Residue "I ASP 974": "OD1" <-> "OD2" Residue "I GLU 987": "OE1" <-> "OE2" Residue "I ASP 993": "OD1" <-> "OD2" Residue "I PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1028": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1050": "OE1" <-> "OE2" Residue "I ASP 1081": "OD1" <-> "OD2" Residue "I ARG 1102": "NH1" <-> "NH2" Residue "I PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1134": "OD1" <-> "OD2" Residue "I PHE 1185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1256": "OE1" <-> "OE2" Residue "I ASP 1279": "OD1" <-> "OD2" Residue "I PHE 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1292": "OD1" <-> "OD2" Residue "I ASP 1308": "OD1" <-> "OD2" Residue "G ARG 122": "NH1" <-> "NH2" Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 25": "OE1" <-> "OE2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K GLU 141": "OE1" <-> "OE2" Residue "K GLU 402": "OE1" <-> "OE2" Residue "K GLU 458": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 133": "OE1" <-> "OE2" Residue "L GLU 331": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 29757 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3048 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain breaks: 6 Chain: "B" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3250 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 4 Chain: "C" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1266 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 3 Chain: "D" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3445 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 24, 'TRANS': 396} Chain breaks: 3 Chain: "E" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2355 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 15, 'TRANS': 272} Chain breaks: 7 Chain: "F" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3134 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain breaks: 1 Chain: "H" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1966 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 10, 'TRANS': 231} Chain: "I" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4242 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 24, 'TRANS': 499} Chain breaks: 8 Chain: "G" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 271 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'UNK:plan-1': 33, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "J" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 482 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain breaks: 3 Chain: "K" Number of atoms: 3131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 387, 3111 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 19, 'TRANS': 367} Chain breaks: 14 Conformer: "B" Number of residues, atoms: 387, 3111 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 19, 'TRANS': 367} Chain breaks: 14 bond proxies already assigned to first conformer: 3145 Chain: "L" Number of atoms: 3167 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 3160 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 17, 'TRANS': 374} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 392, 3160 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 17, 'TRANS': 374} Chain breaks: 5 bond proxies already assigned to first conformer: 3214 Time building chain proxies: 17.90, per 1000 atoms: 0.60 Number of scatterers: 29757 At special positions: 0 Unit cell: (175.007, 228.27, 155.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 5570 8.00 N 5085 7.00 C 19026 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: 11.29 Conformation dependent library (CDL) restraints added in 5.0 seconds 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7078 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 25 sheets defined 57.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.965A pdb=" N MET A 59 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 69 through 106 removed outlier: 4.361A pdb=" N TYR A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.890A pdb=" N PHE A 181 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A 182 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 324 through 339 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 403 through 415 removed outlier: 4.568A pdb=" N LEU A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.501A pdb=" N THR A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 510 Proline residue: A 478 - end of helix removed outlier: 3.516A pdb=" N ASP A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 530 Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 549 through 563 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.732A pdb=" N LYS B 312 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 327 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 339 through 356 Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.652A pdb=" N ALA B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 419 through 423 removed outlier: 4.040A pdb=" N LEU B 422 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE B 423 " --> pdb=" O ARG B 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 419 through 423' Processing helix chain 'B' and resid 437 through 444 Processing helix chain 'B' and resid 451 through 468 Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.699A pdb=" N GLU B 521 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 542 Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.624A pdb=" N LEU B 592 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 615 removed outlier: 3.868A pdb=" N SER B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 610 " --> pdb=" O PRO B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 640 Processing helix chain 'B' and resid 673 through 741 removed outlier: 3.768A pdb=" N ARG B 677 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 678 " --> pdb=" O ASN B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 776 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.631A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 123 removed outlier: 3.592A pdb=" N ASN C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 154 Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.510A pdb=" N ALA C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 177 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 191 Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.544A pdb=" N LYS C 216 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.828A pdb=" N ASP C 235 " --> pdb=" O HIS C 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 312 No H-bonds generated for 'chain 'D' and resid 310 through 312' Processing helix chain 'D' and resid 321 through 327 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.739A pdb=" N ALA D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 removed outlier: 3.554A pdb=" N LEU D 378 " --> pdb=" O ASP D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 444 Processing helix chain 'D' and resid 447 through 469 removed outlier: 3.706A pdb=" N HIS D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 524 removed outlier: 4.046A pdb=" N ASP D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 542 removed outlier: 3.535A pdb=" N GLN D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 554 Processing helix chain 'D' and resid 557 through 566 Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.890A pdb=" N LYS D 593 " --> pdb=" O GLY D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 616 Processing helix chain 'D' and resid 619 through 627 removed outlier: 3.607A pdb=" N VAL D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 648 through 747 removed outlier: 3.672A pdb=" N HIS D 652 " --> pdb=" O LYS D 648 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 653 " --> pdb=" O PRO D 649 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 697 " --> pdb=" O LYS D 693 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS D 702 " --> pdb=" O LEU D 698 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS D 703 " --> pdb=" O ASN D 699 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU D 704 " --> pdb=" O HIS D 700 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 709 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 731 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 732 " --> pdb=" O ASN D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 776 removed outlier: 4.041A pdb=" N LYS D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 50 removed outlier: 3.666A pdb=" N ILE E 35 " --> pdb=" O PRO E 31 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 230 through 241 Processing helix chain 'E' and resid 282 through 296 removed outlier: 3.585A pdb=" N ARG E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 450 through 461 removed outlier: 3.863A pdb=" N GLU E 456 " --> pdb=" O ASN E 452 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 465 through 502 Processing helix chain 'E' and resid 511 through 525 Processing helix chain 'F' and resid 323 through 327 removed outlier: 4.319A pdb=" N TRP F 327 " --> pdb=" O PRO F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 357 Processing helix chain 'F' and resid 370 through 400 Processing helix chain 'F' and resid 441 through 450 Processing helix chain 'F' and resid 487 through 499 Processing helix chain 'F' and resid 502 through 523 removed outlier: 5.393A pdb=" N ASP F 511 " --> pdb=" O GLU F 507 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR F 512 " --> pdb=" O GLN F 508 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN F 520 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F 521 " --> pdb=" O ILE F 517 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 532 Processing helix chain 'F' and resid 571 through 584 removed outlier: 3.529A pdb=" N PHE F 575 " --> pdb=" O CYS F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 611 removed outlier: 3.645A pdb=" N VAL F 590 " --> pdb=" O PRO F 586 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU F 611 " --> pdb=" O SER F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 646 removed outlier: 3.689A pdb=" N LYS F 646 " --> pdb=" O ALA F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 666 Processing helix chain 'H' and resid 427 through 435 Processing helix chain 'H' and resid 465 through 472 Processing helix chain 'H' and resid 489 through 518 removed outlier: 3.516A pdb=" N ASN H 518 " --> pdb=" O ASP H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 557 removed outlier: 3.611A pdb=" N ARG H 526 " --> pdb=" O THR H 522 " (cutoff:3.500A) Proline residue: H 540 - end of helix removed outlier: 3.588A pdb=" N ASN H 557 " --> pdb=" O GLU H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 564 Processing helix chain 'H' and resid 575 through 658 removed outlier: 3.780A pdb=" N ALA H 579 " --> pdb=" O ASN H 575 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 635 " --> pdb=" O HIS H 631 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN H 657 " --> pdb=" O LYS H 653 " (cutoff:3.500A) Processing helix chain 'I' and resid 678 through 693 removed outlier: 3.596A pdb=" N ILE I 682 " --> pdb=" O ASP I 678 " (cutoff:3.500A) Processing helix chain 'I' and resid 698 through 702 Processing helix chain 'I' and resid 707 through 716 Processing helix chain 'I' and resid 718 through 734 Processing helix chain 'I' and resid 746 through 765 removed outlier: 3.959A pdb=" N ASP I 750 " --> pdb=" O PRO I 746 " (cutoff:3.500A) Processing helix chain 'I' and resid 791 through 809 Processing helix chain 'I' and resid 883 through 896 Processing helix chain 'I' and resid 909 through 929 Processing helix chain 'I' and resid 931 through 941 removed outlier: 3.926A pdb=" N ARG I 940 " --> pdb=" O ARG I 936 " (cutoff:3.500A) Processing helix chain 'I' and resid 941 through 957 removed outlier: 3.683A pdb=" N LYS I 945 " --> pdb=" O ASN I 941 " (cutoff:3.500A) Processing helix chain 'I' and resid 958 through 962 removed outlier: 4.351A pdb=" N ASN I 961 " --> pdb=" O HIS I 958 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE I 962 " --> pdb=" O PRO I 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 958 through 962' Processing helix chain 'I' and resid 964 through 983 removed outlier: 3.660A pdb=" N ILE I 968 " --> pdb=" O CYS I 964 " (cutoff:3.500A) Processing helix chain 'I' and resid 990 through 1003 removed outlier: 3.764A pdb=" N CYS I 994 " --> pdb=" O SER I 990 " (cutoff:3.500A) Processing helix chain 'I' and resid 1035 through 1047 removed outlier: 3.742A pdb=" N GLY I1039 " --> pdb=" O TYR I1035 " (cutoff:3.500A) Processing helix chain 'I' and resid 1051 through 1063 Processing helix chain 'I' and resid 1078 through 1094 Processing helix chain 'I' and resid 1103 through 1116 Processing helix chain 'I' and resid 1118 through 1125 removed outlier: 3.810A pdb=" N GLN I1125 " --> pdb=" O GLN I1121 " (cutoff:3.500A) Processing helix chain 'I' and resid 1130 through 1154 Proline residue: I1138 - end of helix Processing helix chain 'I' and resid 1188 through 1195 Processing helix chain 'I' and resid 1199 through 1214 removed outlier: 3.510A pdb=" N GLY I1203 " --> pdb=" O ASN I1199 " (cutoff:3.500A) Processing helix chain 'I' and resid 1233 through 1260 removed outlier: 3.694A pdb=" N ILE I1239 " --> pdb=" O PRO I1235 " (cutoff:3.500A) Processing helix chain 'I' and resid 1264 through 1271 removed outlier: 3.638A pdb=" N LYS I1268 " --> pdb=" O GLU I1264 " (cutoff:3.500A) Processing helix chain 'I' and resid 1278 through 1288 removed outlier: 3.519A pdb=" N ILE I1282 " --> pdb=" O THR I1278 " (cutoff:3.500A) Processing helix chain 'I' and resid 1292 through 1314 Processing helix chain 'J' and resid 3 through 10 Processing helix chain 'K' and resid 52 through 53 No H-bonds generated for 'chain 'K' and resid 52 through 53' Processing helix chain 'K' and resid 55 through 55 No H-bonds generated for 'chain 'K' and resid 55 through 55' Processing helix chain 'K' and resid 56 through 60 Processing helix chain 'K' and resid 79 through 84 Processing helix chain 'K' and resid 87 through 94 Processing helix chain 'K' and resid 115 through 116 No H-bonds generated for 'chain 'K' and resid 115 through 116' Processing helix chain 'K' and resid 118 through 118 No H-bonds generated for 'chain 'K' and resid 118 through 118' Processing helix chain 'K' and resid 119 through 128 Processing helix chain 'K' and resid 140 through 148 Processing helix chain 'K' and resid 176 through 179 Processing helix chain 'K' and resid 185 through 198 Processing helix chain 'K' and resid 199 through 201 No H-bonds generated for 'chain 'K' and resid 199 through 201' Processing helix chain 'K' and resid 216 through 226 Processing helix chain 'K' and resid 226 through 234 Processing helix chain 'K' and resid 242 through 262 removed outlier: 3.719A pdb=" N ILE K 256 " --> pdb=" O GLU K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 285 Processing helix chain 'K' and resid 293 through 296 Processing helix chain 'K' and resid 303 through 315 removed outlier: 4.013A pdb=" N PHE K 309 " --> pdb=" O GLU K 305 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA K 310 " --> pdb=" O CYS K 306 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR K 312 " --> pdb=" O GLN K 308 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU K 313 " --> pdb=" O PHE K 309 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE K 314 " --> pdb=" O ALA K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 316 through 319 Processing helix chain 'K' and resid 324 through 328 Processing helix chain 'K' and resid 331 through 332 No H-bonds generated for 'chain 'K' and resid 331 through 332' Processing helix chain 'K' and resid 334 through 334 No H-bonds generated for 'chain 'K' and resid 334 through 334' Processing helix chain 'K' and resid 335 through 339 Processing helix chain 'K' and resid 381 through 389 removed outlier: 4.341A pdb=" N SER K 386 " --> pdb=" O GLU K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 401 Processing helix chain 'K' and resid 406 through 416 removed outlier: 3.792A pdb=" N ARG K 415 " --> pdb=" O GLU K 411 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 442 Processing helix chain 'K' and resid 448 through 452 removed outlier: 3.941A pdb=" N GLY K 452 " --> pdb=" O TRP K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 464 Processing helix chain 'L' and resid 5 through 8 Processing helix chain 'L' and resid 57 through 61 removed outlier: 3.591A pdb=" N ASN L 60 " --> pdb=" O ASN L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 99 Processing helix chain 'L' and resid 120 through 134 Processing helix chain 'L' and resid 145 through 152 Processing helix chain 'L' and resid 191 through 202 removed outlier: 3.529A pdb=" N ASN L 195 " --> pdb=" O GLY L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 215 Processing helix chain 'L' and resid 275 through 279 Processing helix chain 'L' and resid 295 through 300 Processing helix chain 'L' and resid 302 through 318 Processing helix chain 'L' and resid 322 through 330 removed outlier: 3.646A pdb=" N ALA L 328 " --> pdb=" O ASN L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 342 Processing helix chain 'L' and resid 344 through 358 Processing helix chain 'L' and resid 362 through 373 Processing helix chain 'L' and resid 416 through 423 Processing helix chain 'L' and resid 427 through 441 Processing helix chain 'L' and resid 451 through 455 Processing helix chain 'L' and resid 457 through 465 removed outlier: 3.524A pdb=" N ALA L 460 " --> pdb=" O LYS L 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 283 removed outlier: 4.330A pdb=" N LEU A 438 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 439 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 removed outlier: 3.641A pdb=" N SER A 184 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417 Processing sheet with id=AA5, first strand: chain 'B' and resid 781 through 784 Processing sheet with id=AA6, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA7, first strand: chain 'D' and resid 319 through 320 removed outlier: 4.096A pdb=" N ILE D 319 " --> pdb=" O TYR I 778 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 312 through 313 Processing sheet with id=AA9, first strand: chain 'F' and resid 424 through 427 Processing sheet with id=AB1, first strand: chain 'F' and resid 457 through 464 Processing sheet with id=AB2, first strand: chain 'F' and resid 734 through 735 Processing sheet with id=AB3, first strand: chain 'H' and resid 425 through 426 removed outlier: 6.391A pdb=" N VAL H 425 " --> pdb=" O PHE H 453 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER H 452 " --> pdb=" O TYR I 664 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS H 439 " --> pdb=" O VAL I 661 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN I 663 " --> pdb=" O LYS H 439 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL H 441 " --> pdb=" O ASN I 663 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 478 through 479 Processing sheet with id=AB5, first strand: chain 'J' and resid 25 through 30 Processing sheet with id=AB6, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.407A pdb=" N VAL K 8 " --> pdb=" O VAL K 105 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU K 104 " --> pdb=" O GLN K 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 47 through 48 Processing sheet with id=AB8, first strand: chain 'K' and resid 173 through 174 Processing sheet with id=AB9, first strand: chain 'K' and resid 173 through 174 removed outlier: 6.311A pdb=" N VAL K 392 " --> pdb=" O PHE K 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 287 through 292 Processing sheet with id=AC2, first strand: chain 'L' and resid 35 through 38 removed outlier: 3.659A pdb=" N LEU L 35 " --> pdb=" O VAL L 21 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU L 10 " --> pdb=" O LEU L 112 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE L 114 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE L 12 " --> pdb=" O ILE L 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 51 through 54 Processing sheet with id=AC4, first strand: chain 'L' and resid 68 through 69 Processing sheet with id=AC5, first strand: chain 'L' and resid 178 through 179 Processing sheet with id=AC6, first strand: chain 'L' and resid 178 through 179 Processing sheet with id=AC7, first strand: chain 'L' and resid 282 through 285 1573 hydrogen bonds defined for protein. 4500 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: 11.05 Time building geometry restraints manager: 12.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5959 1.33 - 1.45: 6854 1.45 - 1.57: 17394 1.57 - 1.69: 1 1.69 - 1.81: 126 Bond restraints: 30334 Sorted by residual: bond pdb=" C SER K 380 " pdb=" N PRO K 381 " ideal model delta sigma weight residual 1.335 1.404 -0.069 1.30e-02 5.92e+03 2.79e+01 bond pdb=" N PRO K 381 " pdb=" CD PRO K 381 " ideal model delta sigma weight residual 1.473 1.542 -0.069 1.40e-02 5.10e+03 2.43e+01 bond pdb=" N LEU A 416 " pdb=" CA LEU A 416 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.80e+01 bond pdb=" CA ALA L 326 " pdb=" CB ALA L 326 " ideal model delta sigma weight residual 1.530 1.468 0.061 1.56e-02 4.11e+03 1.55e+01 bond pdb=" N PHE I1276 " pdb=" CA PHE I1276 " ideal model delta sigma weight residual 1.453 1.487 -0.033 9.20e-03 1.18e+04 1.32e+01 ... (remaining 30329 not shown) Histogram of bond angle deviations from ideal: 98.88 - 107.27: 1099 107.27 - 115.66: 18640 115.66 - 124.05: 20471 124.05 - 132.44: 704 132.44 - 140.84: 45 Bond angle restraints: 40959 Sorted by residual: angle pdb=" N ARG F 468 " pdb=" CA ARG F 468 " pdb=" C ARG F 468 " ideal model delta sigma weight residual 108.49 100.91 7.58 1.15e+00 7.56e-01 4.34e+01 angle pdb=" C THR F 357 " pdb=" N ASN F 358 " pdb=" CA ASN F 358 " ideal model delta sigma weight residual 121.54 134.02 -12.48 1.91e+00 2.74e-01 4.27e+01 angle pdb=" C SER K 380 " pdb=" N PRO K 381 " pdb=" CA PRO K 381 " ideal model delta sigma weight residual 118.97 113.10 5.87 1.04e+00 9.25e-01 3.19e+01 angle pdb=" C PHE I1028 " pdb=" N GLN I1029 " pdb=" CA GLN I1029 " ideal model delta sigma weight residual 121.54 132.27 -10.73 1.91e+00 2.74e-01 3.16e+01 angle pdb=" N LYS K 176 " pdb=" CA LYS K 176 " pdb=" C LYS K 176 " ideal model delta sigma weight residual 111.28 117.21 -5.93 1.09e+00 8.42e-01 2.96e+01 ... (remaining 40954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16359 18.00 - 36.00: 1664 36.00 - 54.00: 428 54.00 - 72.00: 110 72.00 - 90.00: 35 Dihedral angle restraints: 18596 sinusoidal: 7780 harmonic: 10816 Sorted by residual: dihedral pdb=" CA ASP F 469 " pdb=" C ASP F 469 " pdb=" N ARG F 470 " pdb=" CA ARG F 470 " ideal model delta harmonic sigma weight residual -180.00 -151.16 -28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ILE A 61 " pdb=" C ILE A 61 " pdb=" N PRO A 62 " pdb=" CA PRO A 62 " ideal model delta harmonic sigma weight residual 180.00 -151.54 -28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ILE F 633 " pdb=" C ILE F 633 " pdb=" N THR F 634 " pdb=" CA THR F 634 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 18593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4240 0.112 - 0.224: 322 0.224 - 0.337: 27 0.337 - 0.449: 2 0.449 - 0.561: 2 Chirality restraints: 4593 Sorted by residual: chirality pdb=" CA PHE L 447 " pdb=" N PHE L 447 " pdb=" C PHE L 447 " pdb=" CB PHE L 447 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CB VAL E 207 " pdb=" CA VAL E 207 " pdb=" CG1 VAL E 207 " pdb=" CG2 VAL E 207 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" CA ILE L 359 " pdb=" N ILE L 359 " pdb=" C ILE L 359 " pdb=" CB ILE L 359 " both_signs ideal model delta sigma weight residual False 2.43 2.86 -0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 4590 not shown) Planarity restraints: 5233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 177 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C GLU C 177 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU C 177 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP C 178 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 866 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.84e+00 pdb=" C GLU I 866 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU I 866 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO I 867 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 550 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.58e+00 pdb=" N PRO E 551 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO E 551 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 551 " -0.033 5.00e-02 4.00e+02 ... (remaining 5230 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3196 2.74 - 3.28: 29022 3.28 - 3.82: 47192 3.82 - 4.36: 57646 4.36 - 4.90: 98618 Nonbonded interactions: 235674 Sorted by model distance: nonbonded pdb=" OE2 GLU F 574 " pdb=" OG1 THR I 790 " model vdw 2.196 2.440 nonbonded pdb=" NZ LYS D 461 " pdb=" OD2 ASP D 465 " model vdw 2.204 2.520 nonbonded pdb=" NH2 ARG B 380 " pdb=" OD1 ASN F 570 " model vdw 2.205 2.520 nonbonded pdb=" OG SER D 311 " pdb=" O TRP D 388 " model vdw 2.211 2.440 nonbonded pdb=" O GLU D 642 " pdb=" OG SER D 645 " model vdw 2.212 2.440 ... (remaining 235669 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 299 through 742 or resid 762 through 781)) selection = (chain 'D' and (resid 299 through 468 or resid 514 through 640 or resid 666 thro \ ugh 742 or resid 762 through 781)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.36 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 10.010 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 76.180 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.150 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.008 0.069 30334 Z= 0.499 Angle : 0.961 15.836 40959 Z= 0.608 Chirality : 0.062 0.561 4593 Planarity : 0.005 0.059 5233 Dihedral : 16.234 89.999 11518 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.79 % Favored : 93.43 % Rotamer Outliers : 6.35 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.13), residues: 3490 helix: -0.38 (0.11), residues: 1888 sheet: -0.46 (0.33), residues: 232 loop : -2.14 (0.15), residues: 1370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 246 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 212 outliers final: 85 residues processed: 441 average time/residue: 1.3199 time to fit residues: 692.2573 Evaluate side-chains 219 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 134 time to evaluate : 3.741 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 81 residues processed: 4 average time/residue: 0.3955 time to fit residues: 7.9041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 279 optimal weight: 30.0000 chunk 108 optimal weight: 0.0060 chunk 170 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 324 optimal weight: 20.0000 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 95 HIS A 153 ASN A 171 ASN A 355 ASN A 358 ASN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN A 549 ASN A 556 ASN A 563 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 522 GLN B 738 ASN ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 303 HIS D 325 GLN D 359 ASN D 394 GLN D 416 HIS D 587 ASN D 640 GLN D 678 GLN D 680 ASN D 690 GLN E 204 GLN E 298 HIS ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 HIS F 434 ASN F 534 GLN F 554 GLN F 556 GLN F 614 ASN H 462 ASN H 564 HIS H 589 HIS I 718 ASN I 765 GLN I 805 ASN I 915 ASN I 970 ASN I 981 ASN ** I1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1036 GLN I1100 ASN I1120 GLN I1284 GLN I1300 GLN K 214 GLN K 230 GLN L 116 HIS B L 142 GLN L 167 HIS L 303 ASN L 304 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 30334 Z= 0.192 Angle : 0.606 14.091 40959 Z= 0.315 Chirality : 0.042 0.182 4593 Planarity : 0.004 0.054 5233 Dihedral : 4.977 32.696 3906 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.62 % Favored : 95.01 % Rotamer Outliers : 5.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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 (0.14), residues: 3490 helix: 1.47 (0.12), residues: 1910 sheet: -0.26 (0.31), residues: 262 loop : -1.71 (0.16), residues: 1318 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 176 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 176 outliers final: 87 residues processed: 331 average time/residue: 1.1268 time to fit residues: 457.7158 Evaluate side-chains 225 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 138 time to evaluate : 3.519 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 86 residues processed: 2 average time/residue: 1.1056 time to fit residues: 7.3474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 chunk 220 optimal weight: 40.0000 chunk 89 optimal weight: 8.9990 chunk 324 optimal weight: 30.0000 chunk 350 optimal weight: 40.0000 chunk 289 optimal weight: 5.9990 chunk 322 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 260 optimal weight: 0.0570 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN D 567 GLN D 587 ASN E 111 HIS E 122 HIS E 317 GLN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 554 GLN I 675 ASN ** I1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1036 GLN K 214 GLN K 286 GLN A L 98 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 30334 Z= 0.258 Angle : 0.595 14.609 40959 Z= 0.307 Chirality : 0.042 0.181 4593 Planarity : 0.004 0.051 5233 Dihedral : 4.765 32.002 3906 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.16 % Favored : 94.46 % Rotamer Outliers : 5.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 0.82 (0.14), residues: 3490 helix: 1.91 (0.12), residues: 1924 sheet: 0.04 (0.32), residues: 260 loop : -1.50 (0.17), residues: 1306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 143 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 171 outliers final: 105 residues processed: 300 average time/residue: 1.1655 time to fit residues: 427.4317 Evaluate side-chains 234 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 129 time to evaluate : 3.425 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 101 residues processed: 4 average time/residue: 0.7455 time to fit residues: 8.8847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 218 optimal weight: 10.0000 chunk 325 optimal weight: 6.9990 chunk 345 optimal weight: 20.0000 chunk 170 optimal weight: 0.7980 chunk 308 optimal weight: 30.0000 chunk 92 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN E 122 HIS ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 GLN F 554 GLN H 431 GLN ** I1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1036 GLN I1100 ASN K 435 GLN L 438 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 30334 Z= 0.307 Angle : 0.610 15.404 40959 Z= 0.313 Chirality : 0.043 0.191 4593 Planarity : 0.005 0.055 5233 Dihedral : 4.742 32.095 3906 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.22 % Favored : 94.41 % Rotamer Outliers : 5.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 0.97 (0.15), residues: 3490 helix: 2.00 (0.12), residues: 1916 sheet: 0.16 (0.32), residues: 259 loop : -1.37 (0.17), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 132 time to evaluate : 5.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 171 outliers final: 112 residues processed: 291 average time/residue: 1.1728 time to fit residues: 426.9166 Evaluate side-chains 241 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 129 time to evaluate : 5.027 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 108 residues processed: 4 average time/residue: 0.8283 time to fit residues: 9.4283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 20.0000 chunk 195 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 294 optimal weight: 40.0000 chunk 238 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 176 optimal weight: 0.6980 chunk 309 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN D 522 GLN E 122 HIS F 448 GLN ** I1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 30334 Z= 0.301 Angle : 0.600 15.756 40959 Z= 0.307 Chirality : 0.043 0.185 4593 Planarity : 0.004 0.055 5233 Dihedral : 4.707 32.342 3906 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.28 % Favored : 94.32 % Rotamer Outliers : 4.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.07 (0.15), residues: 3490 helix: 2.08 (0.12), residues: 1916 sheet: 0.24 (0.32), residues: 259 loop : -1.33 (0.17), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 132 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 113 residues processed: 285 average time/residue: 1.1311 time to fit residues: 401.0875 Evaluate side-chains 238 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 125 time to evaluate : 3.809 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 110 residues processed: 3 average time/residue: 0.9133 time to fit residues: 8.6705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 0.4980 chunk 310 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 345 optimal weight: 8.9990 chunk 286 optimal weight: 7.9990 chunk 159 optimal weight: 0.0980 chunk 28 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN D 522 GLN E 122 HIS F 448 GLN F 482 ASN I1006 GLN I1036 GLN K 418 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 30334 Z= 0.147 Angle : 0.529 14.617 40959 Z= 0.268 Chirality : 0.040 0.177 4593 Planarity : 0.004 0.052 5233 Dihedral : 4.362 33.823 3906 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.42 % Favored : 95.32 % Rotamer Outliers : 4.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.52 (0.15), residues: 3490 helix: 2.49 (0.12), residues: 1923 sheet: 0.56 (0.33), residues: 250 loop : -1.26 (0.17), residues: 1317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 147 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 104 residues processed: 285 average time/residue: 1.1021 time to fit residues: 393.9776 Evaluate side-chains 235 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 131 time to evaluate : 4.004 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 102 residues processed: 3 average time/residue: 0.4397 time to fit residues: 7.7923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 50.0000 chunk 38 optimal weight: 0.8980 chunk 196 optimal weight: 0.0040 chunk 252 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 chunk 290 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 344 optimal weight: 0.0980 chunk 215 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN D 522 GLN E 122 HIS F 448 GLN H 573 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 30334 Z= 0.143 Angle : 0.516 14.384 40959 Z= 0.261 Chirality : 0.040 0.180 4593 Planarity : 0.004 0.051 5233 Dihedral : 4.157 32.505 3906 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.04 % Rotamer Outliers : 4.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.74 (0.15), residues: 3490 helix: 2.66 (0.12), residues: 1930 sheet: 0.71 (0.33), residues: 250 loop : -1.17 (0.17), residues: 1310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 153 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 99 residues processed: 285 average time/residue: 1.0300 time to fit residues: 369.1128 Evaluate side-chains 231 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 132 time to evaluate : 3.733 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 96 residues processed: 4 average time/residue: 0.3946 time to fit residues: 7.4811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 205 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 234 optimal weight: 0.0020 chunk 170 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 GLN D 394 GLN E 38 HIS F 448 GLN I1243 GLN I1284 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 30334 Z= 0.209 Angle : 0.550 15.031 40959 Z= 0.277 Chirality : 0.041 0.197 4593 Planarity : 0.004 0.055 5233 Dihedral : 4.236 32.231 3906 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.96 % Favored : 94.75 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.76 (0.15), residues: 3490 helix: 2.65 (0.12), residues: 1921 sheet: 0.75 (0.34), residues: 250 loop : -1.09 (0.17), residues: 1319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 134 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 104 residues processed: 251 average time/residue: 1.0225 time to fit residues: 324.4990 Evaluate side-chains 231 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 127 time to evaluate : 3.672 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 101 residues processed: 4 average time/residue: 0.4276 time to fit residues: 7.6418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 6.9990 chunk 329 optimal weight: 50.0000 chunk 300 optimal weight: 9.9990 chunk 320 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 303 optimal weight: 10.0000 chunk 319 optimal weight: 30.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN D 522 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 GLN I1284 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 30334 Z= 0.189 Angle : 0.542 14.828 40959 Z= 0.273 Chirality : 0.041 0.178 4593 Planarity : 0.004 0.055 5233 Dihedral : 4.224 32.481 3906 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.79 % Favored : 94.92 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.78 (0.15), residues: 3490 helix: 2.65 (0.12), residues: 1927 sheet: 0.89 (0.34), residues: 248 loop : -1.09 (0.17), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 136 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 104 residues processed: 247 average time/residue: 1.0586 time to fit residues: 327.9835 Evaluate side-chains 232 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 128 time to evaluate : 3.835 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 101 residues processed: 4 average time/residue: 0.4608 time to fit residues: 8.2062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 0.9980 chunk 339 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 355 optimal weight: 2.9990 chunk 327 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 218 optimal weight: 10.0000 chunk 173 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 GLN I1284 GLN K 445 ASN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 30334 Z= 0.178 Angle : 0.544 14.740 40959 Z= 0.274 Chirality : 0.041 0.181 4593 Planarity : 0.004 0.056 5233 Dihedral : 4.180 32.426 3906 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.88 % Favored : 94.87 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.85 (0.15), residues: 3490 helix: 2.70 (0.12), residues: 1927 sheet: 0.98 (0.34), residues: 248 loop : -1.07 (0.17), residues: 1315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 130 time to evaluate : 3.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 104 residues processed: 242 average time/residue: 1.0780 time to fit residues: 329.8222 Evaluate side-chains 230 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 126 time to evaluate : 3.602 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 100 residues processed: 5 average time/residue: 0.6541 time to fit residues: 9.3996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 1.9990 chunk 301 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 283 optimal weight: 0.0980 chunk 118 optimal weight: 0.9990 chunk 291 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN E 224 GLN F 448 GLN I1284 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.149741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096589 restraints weight = 104696.056| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.84 r_work: 0.3047 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 30334 Z= 0.156 Angle : 0.537 14.520 40959 Z= 0.268 Chirality : 0.040 0.179 4593 Planarity : 0.004 0.056 5233 Dihedral : 4.116 32.423 3906 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.59 % Favored : 95.18 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.95 (0.15), residues: 3490 helix: 2.77 (0.12), residues: 1927 sheet: 1.02 (0.35), residues: 248 loop : -1.02 (0.17), residues: 1315 =============================================================================== Job complete usr+sys time: 8554.21 seconds wall clock time: 155 minutes 2.19 seconds (9302.19 seconds total)