Starting phenix.real_space_refine on Wed Feb 21 05:48:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/02_2024/7c4j_30285.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/02_2024/7c4j_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_30285/02_2024/7c4j_30285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/02_2024/7c4j_30285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/02_2024/7c4j_30285.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c4j_30285/02_2024/7c4j_30285.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 17.05, per 1000 atoms: 0.57 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: 11.95 Conformation dependent library (CDL) restraints added in 6.1 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: 2.60 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: 10.82 Time building geometry restraints manager: 12.61 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.720 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 77.790 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.140 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.060 ------------------------------------------------------------------------------- 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 % Allowed : 14.56 % Favored : 79.10 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 419 HIS 0.009 0.001 HIS A 359 PHE 0.019 0.002 PHE L 447 TYR 0.025 0.002 TYR L 454 ARG 0.009 0.001 ARG D 420 *********************** 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 : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 TRP cc_start: 0.6797 (t60) cc_final: 0.6434 (t60) REVERT: A 403 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7169 (tp) REVERT: A 443 GLU cc_start: 0.8281 (pp20) cc_final: 0.7989 (pp20) REVERT: C 165 THR cc_start: 0.8695 (m) cc_final: 0.8494 (p) REVERT: D 522 GLN cc_start: 0.8294 (mm110) cc_final: 0.7787 (tp40) REVERT: D 589 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8220 (pt) REVERT: D 770 PHE cc_start: 0.7367 (m-10) cc_final: 0.7160 (m-10) REVERT: E 123 MET cc_start: 0.8023 (ptt) cc_final: 0.7498 (tmm) REVERT: E 318 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7664 (p90) REVERT: I 932 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7316 (t0) REVERT: I 1106 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8997 (tt) REVERT: K 262 GLU cc_start: 0.1440 (OUTLIER) cc_final: 0.0939 (pt0) REVERT: K 397 SER cc_start: -0.0674 (OUTLIER) cc_final: -0.1063 (t) REVERT: L 34 GLU cc_start: 0.1441 (OUTLIER) cc_final: 0.0397 (mt-10) outliers start: 212 outliers final: 85 residues processed: 441 average time/residue: 1.3107 time to fit residues: 687.8343 Evaluate side-chains 227 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 134 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 775 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 601 SER Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain H residue 447 ASP Chi-restraints excluded: chain H residue 459 SER Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 558 SER Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 713 SER Chi-restraints excluded: chain I residue 736 SER Chi-restraints excluded: chain I residue 741 SER Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 808 THR Chi-restraints excluded: chain I residue 867 PRO Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 932 ASP Chi-restraints excluded: chain I residue 939 SER Chi-restraints excluded: chain I residue 980 SER Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1106 LEU Chi-restraints excluded: chain I residue 1115 SER Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1143 SER Chi-restraints excluded: chain I residue 1192 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain J residue 90 ARG Chi-restraints excluded: chain K residue 122 ARG Chi-restraints excluded: chain K residue 262 GLU Chi-restraints excluded: chain K residue 397 SER Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 54 HIS Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 323 ILE Chi-restraints excluded: chain L residue 438 GLN 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: 1.9990 chunk 144 optimal weight: 6.9990 chunk 279 optimal weight: 30.0000 chunk 108 optimal weight: 0.0270 chunk 170 optimal weight: 0.2980 chunk 208 optimal weight: 0.9990 chunk 324 optimal weight: 20.0000 overall best weight: 0.8442 ------------------------------------------------------------------------------- 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 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 522 GLN D 587 ASN D 640 GLN D 678 GLN D 680 ASN D 690 GLN E 204 GLN E 298 HIS E 317 GLN ** 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: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1705 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= 0.181 Angle : 0.599 14.429 40959 Z= 0.310 Chirality : 0.042 0.174 4593 Planarity : 0.004 0.054 5233 Dihedral : 7.281 111.154 4055 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.53 % Favored : 95.09 % Rotamer: Outliers : 4.22 % Allowed : 17.40 % Favored : 78.38 % 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: 0.32 (0.14), residues: 3490 helix: 1.52 (0.12), residues: 1910 sheet: -0.23 (0.31), residues: 259 loop : -1.71 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 463 HIS 0.015 0.001 HIS L 167 PHE 0.015 0.001 PHE L 82 TYR 0.025 0.001 TYR K 455 ARG 0.005 0.000 ARG K 465 *********************** 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 322 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 181 time to evaluate : 3.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8649 (tt) REVERT: A 267 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7999 (tptt) REVERT: B 303 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.7294 (m-70) REVERT: B 452 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8755 (p) REVERT: B 711 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: D 522 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7859 (tp40) REVERT: D 587 ASN cc_start: 0.5395 (OUTLIER) cc_final: 0.4955 (t0) REVERT: D 589 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8178 (pt) REVERT: E 123 MET cc_start: 0.8079 (ptt) cc_final: 0.7477 (tmm) REVERT: E 206 ILE cc_start: 0.8644 (mp) cc_final: 0.8444 (mp) REVERT: F 357 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8188 (t) REVERT: F 468 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.5986 (mtm-85) REVERT: F 629 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8759 (mpt) REVERT: F 653 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8238 (mt) REVERT: H 434 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6615 (t80) REVERT: I 667 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8533 (mp) REVERT: I 901 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8362 (mmtm) REVERT: G 118 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6798 (ppt170) REVERT: K 204 GLU cc_start: 0.0275 (OUTLIER) cc_final: -0.0241 (mp0) REVERT: K 214 GLN cc_start: 0.2259 (OUTLIER) cc_final: 0.1778 (pt0) REVERT: K 262 GLU cc_start: 0.1293 (OUTLIER) cc_final: 0.0670 (pt0) outliers start: 141 outliers final: 51 residues processed: 303 average time/residue: 1.2075 time to fit residues: 442.4574 Evaluate side-chains 209 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 140 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 711 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 587 ASN Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 749 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 901 LYS Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1106 LEU Chi-restraints excluded: chain I residue 1111 SER Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain K residue 214 GLN Chi-restraints excluded: chain K residue 262 GLU Chi-restraints excluded: chain L residue 323 ILE Chi-restraints excluded: chain L residue 438 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 220 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 324 optimal weight: 50.0000 chunk 350 optimal weight: 40.0000 chunk 289 optimal weight: 4.9990 chunk 322 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 260 optimal weight: 0.2980 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 587 ASN ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN D 567 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 286 GLN A Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30334 Z= 0.284 Angle : 0.606 14.769 40959 Z= 0.312 Chirality : 0.043 0.175 4593 Planarity : 0.004 0.047 5233 Dihedral : 6.539 106.749 3974 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.19 % Favored : 94.43 % Rotamer: Outliers : 4.22 % Allowed : 18.30 % Favored : 77.48 % 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: 0.81 (0.14), residues: 3490 helix: 1.88 (0.12), residues: 1917 sheet: 0.02 (0.32), residues: 258 loop : -1.45 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 156 HIS 0.007 0.001 HIS A 359 PHE 0.017 0.001 PHE I 698 TYR 0.019 0.002 TYR F 360 ARG 0.006 0.000 ARG B 462 *********************** 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 284 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 143 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7291 (m-30) REVERT: A 158 MET cc_start: 0.9036 (ttp) cc_final: 0.8814 (ttt) REVERT: A 298 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7892 (tt) REVERT: A 443 GLU cc_start: 0.8111 (pt0) cc_final: 0.7562 (pt0) REVERT: A 554 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7511 (mtt90) REVERT: B 303 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.7300 (m-70) REVERT: B 711 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: D 522 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7876 (tp40) REVERT: D 589 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8098 (pt) REVERT: E 123 MET cc_start: 0.8065 (ptt) cc_final: 0.7463 (tmm) REVERT: E 327 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.7751 (m110) REVERT: F 629 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8720 (mpt) REVERT: H 434 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6634 (t80) REVERT: G 118 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6650 (ppt170) outliers start: 141 outliers final: 76 residues processed: 271 average time/residue: 1.1805 time to fit residues: 390.4220 Evaluate side-chains 216 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 130 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 711 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 749 VAL Chi-restraints excluded: chain F residue 751 SER Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 447 ASP Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain I residue 659 SER Chi-restraints excluded: chain I residue 665 LYS Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 693 LYS Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 793 ASP Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 932 ASP Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1106 LEU Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1137 SER Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain I residue 1311 THR Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 323 ILE Chi-restraints excluded: chain L residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 20.0000 chunk 244 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 218 optimal weight: 6.9990 chunk 325 optimal weight: 4.9990 chunk 345 optimal weight: 20.0000 chunk 170 optimal weight: 0.8980 chunk 308 optimal weight: 30.0000 chunk 92 optimal weight: 0.0670 overall best weight: 1.0920 ------------------------------------------------------------------------------- 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** ** 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 E 324 HIS F 448 GLN F 554 GLN H 431 GLN ** I1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1036 GLN K 214 GLN K 435 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30334 Z= 0.181 Angle : 0.551 14.587 40959 Z= 0.282 Chirality : 0.041 0.191 4593 Planarity : 0.004 0.050 5233 Dihedral : 5.863 54.180 3963 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.65 % Favored : 95.04 % Rotamer: Outliers : 3.56 % Allowed : 18.96 % Favored : 77.48 % 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: 1.15 (0.15), residues: 3490 helix: 2.19 (0.12), residues: 1922 sheet: 0.22 (0.32), residues: 259 loop : -1.37 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 156 HIS 0.007 0.001 HIS I 792 PHE 0.014 0.001 PHE K 244 TYR 0.037 0.001 TYR K 455 ARG 0.005 0.000 ARG B 462 *********************** 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 262 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 143 time to evaluate : 3.491 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.8993 (ttp) cc_final: 0.8780 (ttt) REVERT: A 298 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7922 (tt) REVERT: B 303 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.7249 (m-70) REVERT: B 452 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8768 (p) REVERT: B 578 ASP cc_start: 0.4976 (OUTLIER) cc_final: 0.4766 (m-30) REVERT: B 711 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: B 763 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.6300 (mp) REVERT: D 448 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7280 (m-30) REVERT: D 522 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7927 (tp40) REVERT: D 589 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8180 (pt) REVERT: E 123 MET cc_start: 0.8015 (ptt) cc_final: 0.7360 (tpp) REVERT: F 468 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6029 (mtm-85) REVERT: F 629 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8719 (mpt) REVERT: F 653 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8242 (mt) REVERT: H 434 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.6676 (t80) REVERT: I 794 LYS cc_start: 0.7242 (mmmm) cc_final: 0.6639 (pptt) REVERT: I 1198 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: G 118 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6810 (ppt170) outliers start: 119 outliers final: 62 residues processed: 249 average time/residue: 1.1436 time to fit residues: 348.7927 Evaluate side-chains 214 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 138 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 711 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 749 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 447 ASP Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain I residue 665 LYS Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1106 LEU Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1137 SER Chi-restraints excluded: chain I residue 1198 GLU Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 358 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 294 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 309 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 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 E 38 HIS F 448 GLN ** I1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1036 GLN I1284 GLN L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30334 Z= 0.273 Angle : 0.582 15.483 40959 Z= 0.297 Chirality : 0.042 0.183 4593 Planarity : 0.004 0.054 5233 Dihedral : 5.771 53.175 3956 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.11 % Favored : 94.55 % Rotamer: Outliers : 3.80 % Allowed : 19.05 % Favored : 77.15 % 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: 1.21 (0.15), residues: 3490 helix: 2.20 (0.12), residues: 1917 sheet: 0.32 (0.32), residues: 259 loop : -1.29 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 156 HIS 0.006 0.001 HIS A 359 PHE 0.017 0.001 PHE I 698 TYR 0.019 0.001 TYR D 576 ARG 0.005 0.000 ARG B 462 *********************** 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 263 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 136 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7216 (m-30) REVERT: A 554 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7180 (mtt180) REVERT: B 578 ASP cc_start: 0.5109 (OUTLIER) cc_final: 0.4902 (m-30) REVERT: B 711 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: B 763 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.6333 (mp) REVERT: C 241 HIS cc_start: 0.3703 (t-90) cc_final: 0.3480 (t-90) REVERT: D 312 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8527 (ttmt) REVERT: D 448 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: D 522 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7918 (tp40) REVERT: D 589 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8253 (pt) REVERT: E 123 MET cc_start: 0.7899 (ptt) cc_final: 0.7355 (tpp) REVERT: F 629 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8691 (mpt) REVERT: H 434 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6752 (t80) REVERT: H 460 HIS cc_start: 0.6365 (OUTLIER) cc_final: 0.6044 (m90) REVERT: I 954 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.8989 (mp) REVERT: I 1308 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7818 (t0) REVERT: G 118 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6717 (ppt170) REVERT: K 204 GLU cc_start: 0.0565 (OUTLIER) cc_final: -0.0091 (mp0) outliers start: 127 outliers final: 73 residues processed: 250 average time/residue: 1.1543 time to fit residues: 355.2857 Evaluate side-chains 215 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 127 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 711 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 749 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain I residue 659 SER Chi-restraints excluded: chain I residue 665 LYS Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 693 LYS Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 932 ASP Chi-restraints excluded: chain I residue 954 LEU Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1106 LEU Chi-restraints excluded: chain I residue 1115 SER Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1137 SER Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain I residue 1308 ASP Chi-restraints excluded: chain I residue 1311 THR Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 323 ILE Chi-restraints excluded: chain L residue 358 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 3.9990 chunk 310 optimal weight: 0.0270 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 345 optimal weight: 10.0000 chunk 286 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** 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** ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN F 448 GLN F 482 ASN I1006 GLN K 418 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30334 Z= 0.146 Angle : 0.520 14.662 40959 Z= 0.264 Chirality : 0.040 0.184 4593 Planarity : 0.004 0.053 5233 Dihedral : 5.446 53.194 3954 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.62 % Favored : 95.18 % Rotamer: Outliers : 3.08 % Allowed : 19.80 % Favored : 77.12 % 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: 1.57 (0.15), residues: 3490 helix: 2.52 (0.12), residues: 1925 sheet: 0.60 (0.33), residues: 250 loop : -1.22 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 156 HIS 0.006 0.001 HIS A 359 PHE 0.016 0.001 PHE K 244 TYR 0.018 0.001 TYR D 576 ARG 0.006 0.000 ARG B 462 *********************** 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 254 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 151 time to evaluate : 3.754 Fit side-chains revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8198 (tptt) REVERT: A 298 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 763 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6276 (mp) REVERT: C 92 ASN cc_start: 0.6640 (OUTLIER) cc_final: 0.6422 (p0) REVERT: C 241 HIS cc_start: 0.3403 (t-90) cc_final: 0.3148 (t-90) REVERT: D 448 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: D 522 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7969 (tp40) REVERT: D 589 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8185 (pt) REVERT: E 123 MET cc_start: 0.7948 (ptt) cc_final: 0.7366 (tpp) REVERT: F 468 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.6035 (mtm-85) REVERT: F 629 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8750 (mpt) REVERT: F 653 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8214 (mt) REVERT: H 434 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6638 (t80) REVERT: H 460 HIS cc_start: 0.6309 (OUTLIER) cc_final: 0.5946 (m90) REVERT: I 1198 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: K 135 VAL cc_start: 0.2221 (OUTLIER) cc_final: 0.1932 (t) outliers start: 103 outliers final: 54 residues processed: 239 average time/residue: 1.0974 time to fit residues: 328.9754 Evaluate side-chains 204 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 137 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 693 LYS Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 932 ASP Chi-restraints excluded: chain I residue 1050 GLU Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1137 SER Chi-restraints excluded: chain I residue 1198 GLU Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 323 ILE 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: 0.5980 chunk 196 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 344 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 411 ASN ** 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** ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN F 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2727 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= 0.172 Angle : 0.530 14.838 40959 Z= 0.267 Chirality : 0.040 0.193 4593 Planarity : 0.004 0.052 5233 Dihedral : 5.185 54.682 3942 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.79 % Favored : 94.98 % Rotamer: Outliers : 2.85 % Allowed : 20.58 % Favored : 76.58 % 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: 1.66 (0.15), residues: 3490 helix: 2.59 (0.12), residues: 1921 sheet: 0.70 (0.33), residues: 250 loop : -1.18 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 156 HIS 0.006 0.001 HIS A 359 PHE 0.016 0.001 PHE K 244 TYR 0.018 0.001 TYR D 576 ARG 0.004 0.000 ARG A 356 *********************** 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 232 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 137 time to evaluate : 3.715 Fit side-chains revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8208 (tptt) REVERT: A 298 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7888 (tt) REVERT: C 241 HIS cc_start: 0.3497 (t-90) cc_final: 0.3220 (t-90) REVERT: D 448 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: D 522 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7992 (tp40) REVERT: D 589 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8146 (pt) REVERT: E 123 MET cc_start: 0.7966 (ptt) cc_final: 0.7431 (tpp) REVERT: E 331 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6443 (mp10) REVERT: F 629 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8790 (mpt) REVERT: H 434 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6667 (t80) REVERT: H 460 HIS cc_start: 0.6338 (OUTLIER) cc_final: 0.5979 (m90) REVERT: K 135 VAL cc_start: 0.2173 (OUTLIER) cc_final: 0.1871 (t) outliers start: 95 outliers final: 58 residues processed: 223 average time/residue: 1.1457 time to fit residues: 315.9323 Evaluate side-chains 199 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 132 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 711 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 932 ASP Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1115 SER Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1137 SER Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 323 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 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 F 448 GLN H 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30334 Z= 0.268 Angle : 0.575 16.038 40959 Z= 0.292 Chirality : 0.042 0.189 4593 Planarity : 0.004 0.057 5233 Dihedral : 5.355 56.622 3941 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.02 % Favored : 94.61 % Rotamer: Outliers : 3.05 % Allowed : 20.58 % Favored : 76.37 % 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: 1.58 (0.15), residues: 3490 helix: 2.48 (0.12), residues: 1914 sheet: 0.66 (0.34), residues: 252 loop : -1.12 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 156 HIS 0.007 0.001 HIS A 359 PHE 0.017 0.001 PHE I 698 TYR 0.018 0.001 TYR D 576 ARG 0.003 0.000 ARG K 465 *********************** 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 234 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 132 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7227 (m-40) REVERT: C 241 HIS cc_start: 0.3573 (t-90) cc_final: 0.3286 (t-90) REVERT: D 448 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: D 522 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7966 (tp40) REVERT: D 589 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8198 (pt) REVERT: E 123 MET cc_start: 0.7953 (ptt) cc_final: 0.7421 (tpp) REVERT: F 629 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8753 (mpt) REVERT: F 653 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8201 (mt) REVERT: H 460 HIS cc_start: 0.6307 (OUTLIER) cc_final: 0.6003 (m90) REVERT: I 1308 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7839 (t0) REVERT: K 135 VAL cc_start: 0.2045 (OUTLIER) cc_final: 0.1712 (t) outliers start: 102 outliers final: 69 residues processed: 223 average time/residue: 1.0696 time to fit residues: 296.4607 Evaluate side-chains 205 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 128 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 711 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 483 GLN Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain I residue 659 SER Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 920 THR Chi-restraints excluded: chain I residue 932 ASP Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1115 SER Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1137 SER Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1308 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 323 ILE 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: 20.0000 chunk 320 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 289 optimal weight: 0.5980 chunk 303 optimal weight: 10.0000 chunk 319 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** 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** ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN F 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30334 Z= 0.155 Angle : 0.527 15.071 40959 Z= 0.266 Chirality : 0.040 0.189 4593 Planarity : 0.004 0.055 5233 Dihedral : 5.131 58.580 3941 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.68 % Favored : 95.09 % Rotamer: Outliers : 2.52 % Allowed : 21.17 % Favored : 76.31 % 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: 1.82 (0.15), residues: 3490 helix: 2.70 (0.12), residues: 1926 sheet: 0.95 (0.35), residues: 242 loop : -1.11 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 229 HIS 0.006 0.001 HIS A 359 PHE 0.016 0.001 PHE K 244 TYR 0.019 0.001 TYR D 576 ARG 0.004 0.000 ARG A 356 *********************** 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 219 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 135 time to evaluate : 4.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.6859 (m-40) REVERT: D 448 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: D 522 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7967 (tp-100) REVERT: D 589 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8115 (pt) REVERT: E 123 MET cc_start: 0.7983 (ptt) cc_final: 0.7207 (tpp) REVERT: F 629 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8781 (mpt) REVERT: F 653 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8198 (mt) REVERT: H 434 TYR cc_start: 0.7400 (m-80) cc_final: 0.6793 (t80) REVERT: H 460 HIS cc_start: 0.6182 (OUTLIER) cc_final: 0.5808 (m90) REVERT: I 659 SER cc_start: 0.6374 (OUTLIER) cc_final: 0.5724 (p) REVERT: K 135 VAL cc_start: 0.2189 (OUTLIER) cc_final: 0.1877 (t) REVERT: K 177 ASN cc_start: 0.1596 (OUTLIER) cc_final: 0.0713 (m-40) outliers start: 84 outliers final: 54 residues processed: 210 average time/residue: 1.0570 time to fit residues: 277.1732 Evaluate side-chains 191 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 128 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 711 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain I residue 659 SER Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 920 THR Chi-restraints excluded: chain I residue 932 ASP Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1137 SER Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 177 ASN Chi-restraints excluded: chain L residue 323 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 0.9990 chunk 339 optimal weight: 20.0000 chunk 206 optimal weight: 0.9990 chunk 160 optimal weight: 0.0980 chunk 235 optimal weight: 2.9990 chunk 355 optimal weight: 0.1980 chunk 327 optimal weight: 0.9990 chunk 283 optimal weight: 0.0370 chunk 29 optimal weight: 0.7980 chunk 218 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 640 GLN B 766 GLN D 394 GLN F 448 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30334 Z= 0.142 Angle : 0.521 14.080 40959 Z= 0.260 Chirality : 0.040 0.182 4593 Planarity : 0.004 0.056 5233 Dihedral : 4.826 58.236 3939 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 1.86 % Allowed : 21.86 % Favored : 76.28 % 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: 2.02 (0.15), residues: 3490 helix: 2.84 (0.12), residues: 1934 sheet: 1.05 (0.35), residues: 241 loop : -1.01 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 229 HIS 0.006 0.001 HIS A 359 PHE 0.016 0.001 PHE K 244 TYR 0.017 0.001 TYR D 576 ARG 0.003 0.000 ARG A 356 ********************** 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 218 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 156 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7414 (ptp) cc_final: 0.7123 (ptt) REVERT: C 229 TRP cc_start: 0.3841 (t-100) cc_final: 0.1897 (t-100) REVERT: D 374 ASP cc_start: 0.8432 (p0) cc_final: 0.8089 (p0) REVERT: D 522 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7907 (tp40) REVERT: D 589 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8078 (pt) REVERT: E 123 MET cc_start: 0.7971 (ptt) cc_final: 0.7228 (tpp) REVERT: F 629 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8740 (mpt) REVERT: F 653 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8201 (mt) REVERT: H 460 HIS cc_start: 0.6042 (OUTLIER) cc_final: 0.5630 (m90) REVERT: K 135 VAL cc_start: 0.2143 (OUTLIER) cc_final: 0.1843 (t) REVERT: K 177 ASN cc_start: 0.1622 (OUTLIER) cc_final: 0.0755 (m-40) outliers start: 62 outliers final: 41 residues processed: 211 average time/residue: 1.2770 time to fit residues: 333.7086 Evaluate side-chains 180 residues out of total 3337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 711 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 932 ASP Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1137 SER Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 177 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 5.9990 chunk 301 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 0.0870 chunk 283 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 291 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 I1213 ASN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.150644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.097827 restraints weight = 105208.744| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.85 r_work: 0.3084 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 30334 Z= 0.239 Angle : 0.648 59.199 40959 Z= 0.361 Chirality : 0.045 1.127 4593 Planarity : 0.004 0.089 5233 Dihedral : 4.693 49.379 3931 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 1.71 % Allowed : 22.25 % Favored : 76.04 % Cbeta Deviations : 0.03 % 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: 2.00 (0.15), residues: 3490 helix: 2.81 (0.12), residues: 1934 sheet: 1.06 (0.35), residues: 241 loop : -1.00 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 229 HIS 0.006 0.001 HIS A 359 PHE 0.040 0.001 PHE A 349 TYR 0.019 0.001 TYR D 576 ARG 0.009 0.000 ARG F 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8485.26 seconds wall clock time: 153 minutes 26.61 seconds (9206.61 seconds total)