Starting phenix.real_space_refine on Sat Mar 23 08:19:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7une_26622/03_2024/7une_26622.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7une_26622/03_2024/7une_26622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7une_26622/03_2024/7une_26622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7une_26622/03_2024/7une_26622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7une_26622/03_2024/7une_26622.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7une_26622/03_2024/7une_26622.pdb" } resolution = 3.73 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= 0.004 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 199 5.16 5 C 22859 2.51 5 N 6303 2.21 5 O 6848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 193": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "L PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 279": "OE1" <-> "OE2" Residue "L ARG 280": "NH1" <-> "NH2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L ARG 338": "NH1" <-> "NH2" Residue "L GLU 356": "OE1" <-> "OE2" Residue "L ASP 371": "OD1" <-> "OD2" Residue "L TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 388": "NH1" <-> "NH2" Residue "L ASP 419": "OD1" <-> "OD2" Residue "L PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 485": "OE1" <-> "OE2" Residue "L GLU 491": "OE1" <-> "OE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L ASP 517": "OD1" <-> "OD2" Residue "L ASP 518": "OD1" <-> "OD2" Residue "L TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 549": "OD1" <-> "OD2" Residue "L PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 600": "OD1" <-> "OD2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 192": "OD1" <-> "OD2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "U PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 20": "OE1" <-> "OE2" Residue "U GLU 23": "OE1" <-> "OE2" Residue "U PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 29": "OD1" <-> "OD2" Residue "U TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 74": "OD1" <-> "OD2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "U PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 118": "OE1" <-> "OE2" Residue "U GLU 131": "OE1" <-> "OE2" Residue "U GLU 154": "OE1" <-> "OE2" Residue "U ASP 172": "OD1" <-> "OD2" Residue "U GLU 197": "OE1" <-> "OE2" Residue "U PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 226": "OD1" <-> "OD2" Residue "U PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 261": "OE1" <-> "OE2" Residue "U PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 273": "OE1" <-> "OE2" Residue "U PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 343": "OD1" <-> "OD2" Residue "U TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 404": "OD1" <-> "OD2" Residue "U GLU 407": "OE1" <-> "OE2" Residue "U GLU 432": "OE1" <-> "OE2" Residue "U GLU 447": "OE1" <-> "OE2" Residue "U ARG 450": "NH1" <-> "NH2" Residue "d ASP 5": "OD1" <-> "OD2" Residue "d PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 20": "OE1" <-> "OE2" Residue "d GLU 22": "OE1" <-> "OE2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ASP 31": "OD1" <-> "OD2" Residue "d GLU 37": "OE1" <-> "OE2" Residue "d GLU 41": "OE1" <-> "OE2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d GLU 55": "OE1" <-> "OE2" Residue "d TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 164": "OD1" <-> "OD2" Residue "d GLU 170": "OE1" <-> "OE2" Residue "d TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 176": "OE1" <-> "OE2" Residue "d ASP 201": "OD1" <-> "OD2" Residue "d PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 77": "OD1" <-> "OD2" Residue "M PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M ASP 290": "OD1" <-> "OD2" Residue "M ARG 338": "NH1" <-> "NH2" Residue "M ASP 349": "OD1" <-> "OD2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "M ARG 388": "NH1" <-> "NH2" Residue "M GLU 399": "OE1" <-> "OE2" Residue "M ASP 416": "OD1" <-> "OD2" Residue "M TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 466": "OD1" <-> "OD2" Residue "M ASP 518": "OD1" <-> "OD2" Residue "M TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 549": "OD1" <-> "OD2" Residue "M ARG 552": "NH1" <-> "NH2" Residue "M ASP 562": "OD1" <-> "OD2" Residue "M GLU 572": "OE1" <-> "OE2" Residue "M ASP 588": "OD1" <-> "OD2" Residue "M ASP 592": "OD1" <-> "OD2" Residue "M GLU 594": "OE1" <-> "OE2" Residue "M ASP 600": "OD1" <-> "OD2" Residue "M ASP 607": "OD1" <-> "OD2" Residue "M ARG 613": "NH1" <-> "NH2" Residue "N TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N GLU 69": "OE1" <-> "OE2" Residue "N ASP 77": "OD1" <-> "OD2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 100": "OD1" <-> "OD2" Residue "N ASP 130": "OD1" <-> "OD2" Residue "N ASP 151": "OD1" <-> "OD2" Residue "N TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 219": "OE1" <-> "OE2" Residue "N TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 289": "NH1" <-> "NH2" Residue "N ASP 290": "OD1" <-> "OD2" Residue "N PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 293": "OE1" <-> "OE2" Residue "N ARG 338": "NH1" <-> "NH2" Residue "N GLU 356": "OE1" <-> "OE2" Residue "N GLU 387": "OE1" <-> "OE2" Residue "N ARG 388": "NH1" <-> "NH2" Residue "N ASP 416": "OD1" <-> "OD2" Residue "N TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 463": "OE1" <-> "OE2" Residue "N TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 466": "OD1" <-> "OD2" Residue "N PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 485": "OE1" <-> "OE2" Residue "N GLU 486": "OE1" <-> "OE2" Residue "N GLU 503": "OE1" <-> "OE2" Residue "N ASP 505": "OD1" <-> "OD2" Residue "N ASP 517": "OD1" <-> "OD2" Residue "N PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 549": "OD1" <-> "OD2" Residue "N GLU 556": "OE1" <-> "OE2" Residue "N TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 594": "OE1" <-> "OE2" Residue "N ASP 600": "OD1" <-> "OD2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 61": "OD1" <-> "OD2" Residue "Q ASP 126": "OD1" <-> "OD2" Residue "Q ASP 149": "OD1" <-> "OD2" Residue "Q PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 239": "OE1" <-> "OE2" Residue "Q GLU 249": "OE1" <-> "OE2" Residue "Q GLU 250": "OE1" <-> "OE2" Residue "Q PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 283": "OE1" <-> "OE2" Residue "Q PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 290": "OE1" <-> "OE2" Residue "Q TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "Q TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 460": "NH1" <-> "NH2" Residue "Q PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 469": "OE1" <-> "OE2" Residue "Q TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 502": "OE1" <-> "OE2" Residue "Q PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 506": "NH1" <-> "NH2" Residue "O TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 149": "OD1" <-> "OD2" Residue "O PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 250": "OE1" <-> "OE2" Residue "O PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 283": "OE1" <-> "OE2" Residue "O PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 342": "OE1" <-> "OE2" Residue "O ASP 380": "OD1" <-> "OD2" Residue "O TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 448": "OD1" <-> "OD2" Residue "O GLU 453": "OE1" <-> "OE2" Residue "O ARG 460": "NH1" <-> "NH2" Residue "O PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 490": "OE1" <-> "OE2" Residue "P TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 152": "OD1" <-> "OD2" Residue "P ASP 255": "OD1" <-> "OD2" Residue "P PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 367": "OD1" <-> "OD2" Residue "P TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 374": "OE1" <-> "OE2" Residue "P ASP 380": "OD1" <-> "OD2" Residue "P ASP 417": "OD1" <-> "OD2" Residue "P GLU 441": "OE1" <-> "OE2" Residue "P GLU 442": "OE1" <-> "OE2" Residue "P ASP 448": "OD1" <-> "OD2" Residue "P TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 460": "NH1" <-> "NH2" Residue "P PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 502": "OE1" <-> "OE2" Residue "P PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 506": "NH1" <-> "NH2" Residue "b ARG 50": "NH1" <-> "NH2" Residue "b TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 162": "OD1" <-> "OD2" Residue "b ASP 168": "OD1" <-> "OD2" Residue "b TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 210": "OE1" <-> "OE2" Residue "b PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 65": "OE1" <-> "OE2" Residue "c ASP 88": "OD1" <-> "OD2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 137": "NH1" <-> "NH2" Residue "c TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 161": "NH1" <-> "NH2" Residue "c ASP 168": "OD1" <-> "OD2" Residue "c TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 175": "OE1" <-> "OE2" Residue "c GLU 176": "OE1" <-> "OE2" Residue "c TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 105": "OD1" <-> "OD2" Residue "g ARG 107": "NH1" <-> "NH2" Residue "e GLU 74": "OE1" <-> "OE2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e ARG 94": "NH1" <-> "NH2" Residue "f ARG 107": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36209 Number of models: 1 Model: "" Number of chains: 14 Chain: "L" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1717 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "U" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3365 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 1 Chain: "d" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1818 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain: "M" Number of atoms: 4619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4619 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 564} Chain breaks: 1 Chain: "N" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4613 Classifications: {'peptide': 593} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 562} Chain breaks: 1 Chain: "Q" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3604 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "O" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "P" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3560 Classifications: {'peptide': 455} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 427} Chain breaks: 1 Chain: "b" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1479 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "c" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1505 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 189} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "g" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 665 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 105} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "e" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 501 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 82 Chain: "f" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 512 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 75} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 90 Time building chain proxies: 18.94, per 1000 atoms: 0.52 Number of scatterers: 36209 At special positions: 0 Unit cell: (212.48, 157.7, 175.13, 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 199 16.00 O 6848 8.00 N 6303 7.00 C 22859 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: 14.28 Conformation dependent library (CDL) restraints added in 6.6 seconds 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8676 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 41 sheets defined 42.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'L' and resid 105 through 113 removed outlier: 3.977A pdb=" N SER L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER L 111 " --> pdb=" O SER L 107 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN L 112 " --> pdb=" O ASP L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 257 No H-bonds generated for 'chain 'L' and resid 255 through 257' Processing helix chain 'L' and resid 258 through 266 removed outlier: 4.051A pdb=" N SER L 264 " --> pdb=" O SER L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 291 removed outlier: 4.094A pdb=" N GLU L 286 " --> pdb=" O ASN L 282 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL L 287 " --> pdb=" O GLU L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 325 Processing helix chain 'L' and resid 326 through 339 removed outlier: 3.541A pdb=" N PHE L 337 " --> pdb=" O LEU L 333 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP L 339 " --> pdb=" O GLU L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 365 removed outlier: 3.776A pdb=" N TRP L 354 " --> pdb=" O SER L 350 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU L 360 " --> pdb=" O GLU L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 382 removed outlier: 3.556A pdb=" N ARG L 381 " --> pdb=" O TYR L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 387 removed outlier: 3.534A pdb=" N GLU L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 419 through 426 removed outlier: 3.598A pdb=" N ALA L 424 " --> pdb=" O PRO L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 458 through 460 No H-bonds generated for 'chain 'L' and resid 458 through 460' Processing helix chain 'L' and resid 461 through 469 removed outlier: 3.504A pdb=" N LYS L 467 " --> pdb=" O GLU L 463 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 486 removed outlier: 3.889A pdb=" N THR L 477 " --> pdb=" O VAL L 473 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU L 481 " --> pdb=" O THR L 477 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU L 483 " --> pdb=" O ALA L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 490 Processing helix chain 'L' and resid 502 through 507 removed outlier: 3.616A pdb=" N ILE L 507 " --> pdb=" O GLU L 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 507 through 519 removed outlier: 4.056A pdb=" N LYS L 513 " --> pdb=" O LEU L 509 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP L 517 " --> pdb=" O LYS L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 545 removed outlier: 3.986A pdb=" N ASN L 543 " --> pdb=" O GLY L 539 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET L 544 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 545 through 557 removed outlier: 3.537A pdb=" N ASP L 549 " --> pdb=" O ILE L 545 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL L 555 " --> pdb=" O ALA L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 567 through 572 Processing helix chain 'L' and resid 574 through 582 removed outlier: 3.768A pdb=" N TYR L 579 " --> pdb=" O GLY L 575 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER L 582 " --> pdb=" O LEU L 578 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 587 removed outlier: 3.825A pdb=" N LYS L 587 " --> pdb=" O MET L 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 593 through 613 removed outlier: 3.793A pdb=" N LEU L 605 " --> pdb=" O TYR L 601 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG L 613 " --> pdb=" O GLN L 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 65 removed outlier: 3.612A pdb=" N THR D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 23 " --> pdb=" O MET D 19 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY D 29 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG D 63 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 77 removed outlier: 4.839A pdb=" N THR D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 86 removed outlier: 3.578A pdb=" N VAL D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 174 removed outlier: 3.535A pdb=" N ALA D 132 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 removed outlier: 3.627A pdb=" N ARG D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP D 192 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 29 removed outlier: 4.160A pdb=" N GLU U 23 " --> pdb=" O GLU U 19 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP U 25 " --> pdb=" O GLN U 21 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU U 27 " --> pdb=" O GLU U 23 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 51 removed outlier: 3.882A pdb=" N LEU U 50 " --> pdb=" O SER U 46 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN U 51 " --> pdb=" O LEU U 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 46 through 51' Processing helix chain 'U' and resid 59 through 71 removed outlier: 3.554A pdb=" N VAL U 63 " --> pdb=" O PRO U 59 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR U 64 " --> pdb=" O PRO U 60 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG U 65 " --> pdb=" O GLU U 61 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET U 70 " --> pdb=" O LEU U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 99 removed outlier: 3.690A pdb=" N ALA U 93 " --> pdb=" O GLU U 89 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER U 94 " --> pdb=" O GLN U 90 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 107 removed outlier: 3.609A pdb=" N SER U 107 " --> pdb=" O SER U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 112 Processing helix chain 'U' and resid 124 through 144 removed outlier: 3.537A pdb=" N LYS U 128 " --> pdb=" O ARG U 124 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL U 134 " --> pdb=" O THR U 130 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY U 135 " --> pdb=" O GLU U 131 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER U 136 " --> pdb=" O ASP U 132 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL U 138 " --> pdb=" O VAL U 134 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS U 139 " --> pdb=" O GLY U 135 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER U 142 " --> pdb=" O VAL U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 170 removed outlier: 3.656A pdb=" N GLN U 163 " --> pdb=" O ASN U 159 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN U 168 " --> pdb=" O VAL U 164 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU U 169 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU U 170 " --> pdb=" O ALA U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 187 removed outlier: 4.235A pdb=" N LEU U 187 " --> pdb=" O PRO U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 192 through 197 removed outlier: 3.691A pdb=" N GLU U 197 " --> pdb=" O ARG U 193 " (cutoff:3.500A) Processing helix chain 'U' and resid 198 through 203 Processing helix chain 'U' and resid 203 through 209 removed outlier: 3.987A pdb=" N ALA U 207 " --> pdb=" O VAL U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 218 removed outlier: 3.561A pdb=" N ILE U 214 " --> pdb=" O LEU U 210 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS U 215 " --> pdb=" O SER U 211 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS U 216 " --> pdb=" O VAL U 212 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY U 217 " --> pdb=" O VAL U 213 " (cutoff:3.500A) Processing helix chain 'U' and resid 247 through 255 removed outlier: 3.665A pdb=" N ASN U 255 " --> pdb=" O VAL U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 259 through 263 removed outlier: 3.532A pdb=" N GLN U 262 " --> pdb=" O PRO U 259 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG U 263 " --> pdb=" O ARG U 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 259 through 263' Processing helix chain 'U' and resid 278 through 286 Processing helix chain 'U' and resid 432 through 440 Processing helix chain 'd' and resid 4 through 12 removed outlier: 3.527A pdb=" N VAL d 8 " --> pdb=" O SER d 4 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS d 10 " --> pdb=" O ALA d 6 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN d 11 " --> pdb=" O ASP d 7 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 32 through 47 removed outlier: 3.805A pdb=" N GLU d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU d 37 " --> pdb=" O LYS d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 72 removed outlier: 3.555A pdb=" N LYS d 62 " --> pdb=" O GLU d 58 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU d 65 " --> pdb=" O GLU d 61 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE d 70 " --> pdb=" O GLN d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 87 removed outlier: 4.137A pdb=" N LYS d 82 " --> pdb=" O GLN d 78 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG d 85 " --> pdb=" O LEU d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 108 removed outlier: 3.603A pdb=" N LYS d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG d 101 " --> pdb=" O GLU d 97 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS d 104 " --> pdb=" O GLN d 100 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL d 105 " --> pdb=" O ARG d 101 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL d 106 " --> pdb=" O LEU d 102 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP d 108 " --> pdb=" O LYS d 104 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 128 removed outlier: 3.928A pdb=" N VAL d 114 " --> pdb=" O THR d 110 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY d 118 " --> pdb=" O VAL d 114 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY d 123 " --> pdb=" O LEU d 119 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN d 126 " --> pdb=" O GLN d 122 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU d 128 " --> pdb=" O LEU d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 149 removed outlier: 3.533A pdb=" N ALA d 146 " --> pdb=" O PRO d 142 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA d 147 " --> pdb=" O LEU d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 150 through 156 removed outlier: 4.033A pdb=" N VAL d 154 " --> pdb=" O LYS d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 216 removed outlier: 3.802A pdb=" N ASP d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU d 202 " --> pdb=" O SER d 198 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN d 205 " --> pdb=" O ASP d 201 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN d 206 " --> pdb=" O LEU d 202 " (cutoff:3.500A) Proline residue: d 209 - end of helix Processing helix chain 'M' and resid 105 through 113 removed outlier: 4.195A pdb=" N SER M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR M 113 " --> pdb=" O ILE M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 265 removed outlier: 3.776A pdb=" N GLN M 261 " --> pdb=" O THR M 257 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER M 262 " --> pdb=" O VAL M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 291 removed outlier: 3.550A pdb=" N VAL M 287 " --> pdb=" O GLU M 283 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 288 " --> pdb=" O MET M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 339 removed outlier: 3.650A pdb=" N GLU M 324 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER M 326 " --> pdb=" O ALA M 322 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE M 327 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR M 328 " --> pdb=" O GLU M 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP M 339 " --> pdb=" O GLU M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 364 Processing helix chain 'M' and resid 377 through 382 Processing helix chain 'M' and resid 382 through 387 Processing helix chain 'M' and resid 412 through 416 removed outlier: 3.948A pdb=" N GLY M 415 " --> pdb=" O PRO M 412 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP M 416 " --> pdb=" O PRO M 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 412 through 416' Processing helix chain 'M' and resid 421 through 426 Processing helix chain 'M' and resid 461 through 469 removed outlier: 3.698A pdb=" N LYS M 467 " --> pdb=" O GLU M 463 " (cutoff:3.500A) Processing helix chain 'M' and resid 471 through 494 removed outlier: 3.770A pdb=" N LEU M 475 " --> pdb=" O GLU M 471 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS M 478 " --> pdb=" O PRO M 474 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU M 483 " --> pdb=" O ALA M 479 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP M 488 " --> pdb=" O GLN M 484 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU M 491 " --> pdb=" O GLU M 487 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE M 492 " --> pdb=" O ASP M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 507 through 519 removed outlier: 3.573A pdb=" N ALA M 512 " --> pdb=" O THR M 508 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS M 513 " --> pdb=" O LEU M 509 " (cutoff:3.500A) Processing helix chain 'M' and resid 533 through 557 removed outlier: 3.562A pdb=" N ASN M 543 " --> pdb=" O GLY M 539 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET M 544 " --> pdb=" O MET M 540 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU M 556 " --> pdb=" O ARG M 552 " (cutoff:3.500A) Processing helix chain 'M' and resid 566 through 574 removed outlier: 3.637A pdb=" N ILE M 570 " --> pdb=" O THR M 566 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS M 573 " --> pdb=" O ILE M 569 " (cutoff:3.500A) Processing helix chain 'M' and resid 576 through 582 Processing helix chain 'M' and resid 597 through 609 removed outlier: 3.611A pdb=" N ALA M 602 " --> pdb=" O LYS M 598 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN M 603 " --> pdb=" O ALA M 599 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU M 604 " --> pdb=" O ASP M 600 " (cutoff:3.500A) Processing helix chain 'M' and resid 610 through 612 No H-bonds generated for 'chain 'M' and resid 610 through 612' Processing helix chain 'N' and resid 105 through 113 removed outlier: 3.565A pdb=" N SER N 110 " --> pdb=" O LEU N 106 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 266 removed outlier: 3.734A pdb=" N LEU N 263 " --> pdb=" O ILE N 259 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS N 265 " --> pdb=" O GLN N 261 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR N 266 " --> pdb=" O SER N 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 280 through 291 removed outlier: 4.227A pdb=" N VAL N 287 " --> pdb=" O GLU N 283 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG N 289 " --> pdb=" O SER N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 340 removed outlier: 3.553A pdb=" N GLU N 324 " --> pdb=" O VAL N 320 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA N 325 " --> pdb=" O ALA N 321 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER N 326 " --> pdb=" O ALA N 322 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE N 327 " --> pdb=" O ARG N 323 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR N 328 " --> pdb=" O GLU N 324 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE N 337 " --> pdb=" O LEU N 333 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET N 340 " --> pdb=" O TYR N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 365 removed outlier: 3.849A pdb=" N GLU N 360 " --> pdb=" O GLU N 356 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 387 removed outlier: 3.518A pdb=" N GLU N 387 " --> pdb=" O ALA N 383 " (cutoff:3.500A) Processing helix chain 'N' and resid 437 through 441 removed outlier: 4.106A pdb=" N GLN N 441 " --> pdb=" O LYS N 438 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 462 removed outlier: 3.563A pdb=" N ASP N 462 " --> pdb=" O ARG N 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 459 through 462' Processing helix chain 'N' and resid 463 through 469 Processing helix chain 'N' and resid 471 through 486 removed outlier: 3.982A pdb=" N LEU N 475 " --> pdb=" O GLU N 471 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU N 481 " --> pdb=" O THR N 477 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU N 483 " --> pdb=" O ALA N 479 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN N 484 " --> pdb=" O LYS N 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 486 through 496 removed outlier: 3.831A pdb=" N GLU N 491 " --> pdb=" O GLU N 487 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE N 492 " --> pdb=" O ASP N 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 506 through 519 removed outlier: 4.607A pdb=" N ALA N 512 " --> pdb=" O THR N 508 " (cutoff:3.500A) Processing helix chain 'N' and resid 533 through 558 removed outlier: 3.624A pdb=" N LEU N 541 " --> pdb=" O THR N 537 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN N 543 " --> pdb=" O GLY N 539 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA N 546 " --> pdb=" O SER N 542 " (cutoff:3.500A) Processing helix chain 'N' and resid 566 through 568 No H-bonds generated for 'chain 'N' and resid 566 through 568' Processing helix chain 'N' and resid 569 through 574 removed outlier: 3.734A pdb=" N HIS N 573 " --> pdb=" O ILE N 569 " (cutoff:3.500A) Processing helix chain 'N' and resid 576 through 581 removed outlier: 3.710A pdb=" N LYS N 580 " --> pdb=" O GLU N 576 " (cutoff:3.500A) Processing helix chain 'N' and resid 599 through 604 Processing helix chain 'N' and resid 605 through 610 Processing helix chain 'N' and resid 611 through 615 Processing helix chain 'Q' and resid 124 through 128 removed outlier: 3.919A pdb=" N MET Q 127 " --> pdb=" O SER Q 124 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU Q 128 " --> pdb=" O GLU Q 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 124 through 128' Processing helix chain 'Q' and resid 159 through 161 No H-bonds generated for 'chain 'Q' and resid 159 through 161' Processing helix chain 'Q' and resid 174 through 179 Processing helix chain 'Q' and resid 200 through 210 Processing helix chain 'Q' and resid 237 through 246 Processing helix chain 'Q' and resid 269 through 286 Proline residue: Q 275 - end of helix removed outlier: 3.709A pdb=" N LEU Q 279 " --> pdb=" O PRO Q 275 " (cutoff:3.500A) Processing helix chain 'Q' and resid 300 through 314 removed outlier: 3.540A pdb=" N ARG Q 314 " --> pdb=" O VAL Q 310 " (cutoff:3.500A) Processing helix chain 'Q' and resid 319 through 323 removed outlier: 4.003A pdb=" N GLY Q 322 " --> pdb=" O GLY Q 319 " (cutoff:3.500A) Processing helix chain 'Q' and resid 324 through 325 No H-bonds generated for 'chain 'Q' and resid 324 through 325' Processing helix chain 'Q' and resid 326 through 336 removed outlier: 3.930A pdb=" N ILE Q 334 " --> pdb=" O ASP Q 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 356 through 360 Processing helix chain 'Q' and resid 363 through 370 Processing helix chain 'Q' and resid 414 through 440 removed outlier: 4.003A pdb=" N ASN Q 420 " --> pdb=" O ALA Q 416 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA Q 424 " --> pdb=" O ASN Q 420 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY Q 429 " --> pdb=" O CYS Q 425 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA Q 437 " --> pdb=" O GLN Q 433 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL Q 438 " --> pdb=" O ALA Q 434 " (cutoff:3.500A) Processing helix chain 'Q' and resid 449 through 462 removed outlier: 3.683A pdb=" N LEU Q 455 " --> pdb=" O TYR Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 473 through 485 removed outlier: 3.560A pdb=" N ASP Q 478 " --> pdb=" O TYR Q 474 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE Q 479 " --> pdb=" O GLU Q 475 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN Q 482 " --> pdb=" O ASP Q 478 " (cutoff:3.500A) Processing helix chain 'Q' and resid 496 through 504 removed outlier: 4.596A pdb=" N GLU Q 502 " --> pdb=" O SER Q 498 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 128 removed outlier: 3.735A pdb=" N MET O 127 " --> pdb=" O SER O 124 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU O 128 " --> pdb=" O GLU O 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 124 through 128' Processing helix chain 'O' and resid 159 through 161 No H-bonds generated for 'chain 'O' and resid 159 through 161' Processing helix chain 'O' and resid 174 through 179 Processing helix chain 'O' and resid 198 through 210 removed outlier: 3.523A pdb=" N GLN O 209 " --> pdb=" O GLN O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 251 removed outlier: 3.622A pdb=" N PHE O 243 " --> pdb=" O GLU O 239 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER O 246 " --> pdb=" O ARG O 242 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU O 249 " --> pdb=" O LYS O 245 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 288 removed outlier: 3.582A pdb=" N TYR O 287 " --> pdb=" O GLU O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 313 removed outlier: 3.527A pdb=" N ALA O 304 " --> pdb=" O MET O 300 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU O 309 " --> pdb=" O GLU O 305 " (cutoff:3.500A) Processing helix chain 'O' and resid 319 through 323 Processing helix chain 'O' and resid 324 through 326 No H-bonds generated for 'chain 'O' and resid 324 through 326' Processing helix chain 'O' and resid 327 through 336 removed outlier: 4.020A pdb=" N THR O 333 " --> pdb=" O THR O 329 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE O 334 " --> pdb=" O ASP O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 360 Processing helix chain 'O' and resid 363 through 373 removed outlier: 3.554A pdb=" N LEU O 368 " --> pdb=" O PRO O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 385 removed outlier: 3.597A pdb=" N HIS O 384 " --> pdb=" O ASP O 380 " (cutoff:3.500A) Processing helix chain 'O' and resid 401 through 406 removed outlier: 3.573A pdb=" N ILE O 406 " --> pdb=" O MET O 402 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 440 removed outlier: 3.617A pdb=" N SER O 419 " --> pdb=" O HIS O 415 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN O 420 " --> pdb=" O ALA O 416 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN O 421 " --> pdb=" O ASP O 417 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA O 434 " --> pdb=" O LYS O 430 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA O 437 " --> pdb=" O GLN O 433 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL O 438 " --> pdb=" O ALA O 434 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 459 removed outlier: 3.780A pdb=" N LYS O 457 " --> pdb=" O GLU O 453 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU O 459 " --> pdb=" O LEU O 455 " (cutoff:3.500A) Processing helix chain 'O' and resid 474 through 482 removed outlier: 3.926A pdb=" N ASP O 478 " --> pdb=" O TYR O 474 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY O 480 " --> pdb=" O THR O 476 " (cutoff:3.500A) Processing helix chain 'O' and resid 496 through 504 removed outlier: 3.812A pdb=" N GLU O 502 " --> pdb=" O SER O 498 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 161 No H-bonds generated for 'chain 'P' and resid 159 through 161' Processing helix chain 'P' and resid 198 through 210 Processing helix chain 'P' and resid 237 through 251 Processing helix chain 'P' and resid 253 through 255 No H-bonds generated for 'chain 'P' and resid 253 through 255' Processing helix chain 'P' and resid 267 through 272 removed outlier: 3.678A pdb=" N GLU P 270 " --> pdb=" O PRO P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 288 removed outlier: 3.614A pdb=" N THR P 281 " --> pdb=" O LEU P 277 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR P 287 " --> pdb=" O GLU P 283 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 313 removed outlier: 3.623A pdb=" N ALA P 304 " --> pdb=" O MET P 300 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA P 306 " --> pdb=" O SER P 302 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL P 310 " --> pdb=" O ALA P 306 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA P 313 " --> pdb=" O GLU P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 319 through 323 removed outlier: 3.656A pdb=" N GLY P 322 " --> pdb=" O GLY P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 324 through 325 No H-bonds generated for 'chain 'P' and resid 324 through 325' Processing helix chain 'P' and resid 326 through 336 removed outlier: 3.647A pdb=" N GLU P 336 " --> pdb=" O ALA P 332 " (cutoff:3.500A) Processing helix chain 'P' and resid 356 through 360 Processing helix chain 'P' and resid 363 through 370 Processing helix chain 'P' and resid 381 through 386 removed outlier: 3.608A pdb=" N ARG P 386 " --> pdb=" O GLN P 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 440 removed outlier: 3.649A pdb=" N ASN P 420 " --> pdb=" O ALA P 416 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA P 424 " --> pdb=" O ASN P 420 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP P 431 " --> pdb=" O ALA P 427 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA P 434 " --> pdb=" O LYS P 430 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL P 438 " --> pdb=" O ALA P 434 " (cutoff:3.500A) Processing helix chain 'P' and resid 450 through 462 removed outlier: 3.627A pdb=" N LEU P 455 " --> pdb=" O TYR P 451 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN P 456 " --> pdb=" O LEU P 452 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU P 459 " --> pdb=" O LEU P 455 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG P 460 " --> pdb=" O GLN P 456 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN P 461 " --> pdb=" O LYS P 457 " (cutoff:3.500A) Processing helix chain 'P' and resid 472 through 483 removed outlier: 3.577A pdb=" N LEU P 477 " --> pdb=" O VAL P 473 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN P 482 " --> pdb=" O ASP P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 488 through 492 removed outlier: 3.536A pdb=" N MET P 491 " --> pdb=" O PRO P 488 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU P 492 " --> pdb=" O LYS P 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 488 through 492' Processing helix chain 'P' and resid 496 through 504 removed outlier: 4.485A pdb=" N GLU P 502 " --> pdb=" O SER P 498 " (cutoff:3.500A) Processing helix chain 'b' and resid 47 through 59 removed outlier: 3.675A pdb=" N LEU b 51 " --> pdb=" O GLN b 47 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE b 53 " --> pdb=" O GLN b 49 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR b 56 " --> pdb=" O LYS b 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS b 59 " --> pdb=" O GLU b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 60 through 101 removed outlier: 3.795A pdb=" N GLU b 65 " --> pdb=" O GLU b 61 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN b 66 " --> pdb=" O LYS b 62 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN b 71 " --> pdb=" O GLN b 67 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN b 78 " --> pdb=" O ASN b 74 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU b 90 " --> pdb=" O ALA b 86 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE b 91 " --> pdb=" O ARG b 87 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN b 96 " --> pdb=" O THR b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 112 through 128 removed outlier: 4.069A pdb=" N GLY b 118 " --> pdb=" O VAL b 114 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU b 121 " --> pdb=" O ASP b 117 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU b 128 " --> pdb=" O LEU b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 140 through 150 removed outlier: 3.580A pdb=" N ALA b 147 " --> pdb=" O LEU b 143 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS b 150 " --> pdb=" O ALA b 146 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 160 removed outlier: 3.715A pdb=" N ALA b 158 " --> pdb=" O VAL b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 206 removed outlier: 3.756A pdb=" N LEU b 202 " --> pdb=" O SER b 198 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN b 205 " --> pdb=" O ASP b 201 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN b 206 " --> pdb=" O LEU b 202 " (cutoff:3.500A) Processing helix chain 'b' and resid 207 through 216 Processing helix chain 'c' and resid 33 through 102 removed outlier: 4.269A pdb=" N GLU c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE c 38 " --> pdb=" O ALA c 34 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN c 39 " --> pdb=" O GLU c 35 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU c 41 " --> pdb=" O GLU c 37 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY c 43 " --> pdb=" O ASN c 39 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU c 45 " --> pdb=" O GLU c 41 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL c 46 " --> pdb=" O LYS c 42 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN c 49 " --> pdb=" O LEU c 45 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU c 51 " --> pdb=" O GLN c 47 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS c 52 " --> pdb=" O THR c 48 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU c 55 " --> pdb=" O LEU c 51 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR c 57 " --> pdb=" O ILE c 53 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU c 58 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS c 62 " --> pdb=" O GLU c 58 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG c 80 " --> pdb=" O MET c 76 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN c 100 " --> pdb=" O ASN c 96 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 127 removed outlier: 4.146A pdb=" N GLY c 118 " --> pdb=" O VAL c 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU c 121 " --> pdb=" O ASP c 117 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY c 123 " --> pdb=" O LEU c 119 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 140 through 149 removed outlier: 3.639A pdb=" N ALA c 146 " --> pdb=" O PRO c 142 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN c 149 " --> pdb=" O LYS c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 151 through 158 removed outlier: 3.788A pdb=" N VAL c 157 " --> pdb=" O PRO c 153 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 204 Processing helix chain 'c' and resid 207 through 216 Processing helix chain 'g' and resid 10 through 20 removed outlier: 3.891A pdb=" N ARG g 17 " --> pdb=" O GLN g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 28 through 33 removed outlier: 3.657A pdb=" N LEU g 33 " --> pdb=" O LYS g 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 45 Processing helix chain 'g' and resid 47 through 66 removed outlier: 3.753A pdb=" N GLN g 53 " --> pdb=" O ARG g 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 72 removed outlier: 3.774A pdb=" N ALA g 71 " --> pdb=" O ASN g 68 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU g 72 " --> pdb=" O LEU g 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 68 through 72' Processing helix chain 'g' and resid 77 through 90 removed outlier: 3.778A pdb=" N SER g 86 " --> pdb=" O GLN g 82 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER g 87 " --> pdb=" O GLY g 83 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN g 89 " --> pdb=" O GLN g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 104 removed outlier: 3.869A pdb=" N ALA g 97 " --> pdb=" O GLU g 93 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS g 104 " --> pdb=" O LEU g 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 43 Processing helix chain 'e' and resid 46 through 50 Processing helix chain 'e' and resid 51 through 56 Processing helix chain 'e' and resid 56 through 87 removed outlier: 3.555A pdb=" N GLN e 60 " --> pdb=" O GLN e 56 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA e 61 " --> pdb=" O SER e 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET e 63 " --> pdb=" O GLN e 59 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER e 65 " --> pdb=" O ALA e 61 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN e 66 " --> pdb=" O ALA e 62 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY e 67 " --> pdb=" O MET e 63 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN e 68 " --> pdb=" O GLY e 64 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER e 70 " --> pdb=" O GLN e 66 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA e 71 " --> pdb=" O GLY e 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU e 72 " --> pdb=" O ASN e 68 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL e 73 " --> pdb=" O LEU e 69 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL e 81 " --> pdb=" O THR e 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET e 84 " --> pdb=" O GLN e 80 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER e 87 " --> pdb=" O GLY e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 91 through 104 removed outlier: 3.598A pdb=" N ALA e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 55 Processing helix chain 'f' and resid 59 through 68 removed outlier: 3.692A pdb=" N SER f 65 " --> pdb=" O ALA f 61 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN f 66 " --> pdb=" O ALA f 62 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 85 removed outlier: 3.877A pdb=" N GLU f 72 " --> pdb=" O ASN f 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR f 77 " --> pdb=" O VAL f 73 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG f 78 " --> pdb=" O GLU f 74 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG f 79 " --> pdb=" O GLN f 75 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN f 80 " --> pdb=" O ALA f 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 18 through 25 removed outlier: 6.849A pdb=" N THR L 30 " --> pdb=" O HIS L 22 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL L 24 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL L 28 " --> pdb=" O VAL L 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 28 through 32 current: chain 'L' and resid 50 through 58 removed outlier: 5.953A pdb=" N ILE L 54 " --> pdb=" O GLN L 65 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN L 65 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG L 56 " --> pdb=" O THR L 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 61 through 66 current: chain 'd' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 164 through 167 current: chain 'd' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 190 through 195 current: chain 'M' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 28 through 32 current: chain 'M' and resid 50 through 58 removed outlier: 6.497A pdb=" N THR M 63 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU M 57 " --> pdb=" O MET M 61 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 61 through 66 current: chain 'Q' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 57 through 60 current: chain 'Q' and resid 84 through 90 removed outlier: 6.760A pdb=" N VAL Q 95 " --> pdb=" O LEU Q 87 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL Q 89 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS Q 93 " --> pdb=" O VAL Q 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 93 through 98 current: chain 'P' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 60 current: chain 'P' and resid 81 through 90 removed outlier: 6.622A pdb=" N VAL P 95 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL P 89 " --> pdb=" O LYS P 93 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS P 93 " --> pdb=" O VAL P 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain 'L' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 98 through 99 current: chain 'L' and resid 309 through 315 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 309 through 315 current: chain 'L' and resid 401 through 407 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 164 through 167 removed outlier: 6.452A pdb=" N HIS L 164 " --> pdb=" O ILE L 155 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE L 155 " --> pdb=" O HIS L 164 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE L 166 " --> pdb=" O TYR L 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 146 through 147 removed outlier: 6.674A pdb=" N GLU L 193 " --> pdb=" O THR L 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 295 through 297 Processing sheet with id=AA7, first strand: chain 'L' and resid 431 through 432 Processing sheet with id=AA8, first strand: chain 'D' and resid 92 through 98 Processing sheet with id=AA9, first strand: chain 'U' and resid 44 through 45 removed outlier: 3.560A pdb=" N VAL U 86 " --> pdb=" O PHE U 45 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 121 through 122 Processing sheet with id=AB2, first strand: chain 'U' and resid 233 through 235 removed outlier: 6.053A pdb=" N GLU U 233 " --> pdb=" O TRP U 266 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU U 268 " --> pdb=" O GLU U 233 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLN U 235 " --> pdb=" O LEU U 268 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE U 270 " --> pdb=" O GLN U 235 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU U 268 " --> pdb=" O ALA U 410 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA U 410 " --> pdb=" O LEU U 268 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS U 405 " --> pdb=" O GLU U 297 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY U 305 " --> pdb=" O PHE U 327 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA U 334 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 315 through 319 removed outlier: 6.266A pdb=" N GLN U 317 " --> pdb=" O LEU U 348 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU U 348 " --> pdb=" O GLN U 317 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 87 through 90 Processing sheet with id=AB5, first strand: chain 'M' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 98 through 99 current: chain 'M' and resid 309 through 315 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 309 through 315 current: chain 'M' and resid 403 through 407 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'M' and resid 133 through 134 Processing sheet with id=AB7, first strand: chain 'M' and resid 146 through 147 Processing sheet with id=AB8, first strand: chain 'M' and resid 152 through 157 removed outlier: 3.516A pdb=" N GLY M 154 " --> pdb=" O ILE M 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 226 through 227 removed outlier: 4.645A pdb=" N CYS M 240 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 295 through 297 Processing sheet with id=AC2, first strand: chain 'M' and resid 431 through 432 Processing sheet with id=AC3, first strand: chain 'b' and resid 166 through 167 removed outlier: 3.583A pdb=" N LYS b 191 " --> pdb=" O THR O 46 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU O 45 " --> pdb=" O PHE O 114 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE O 71 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU O 70 " --> pdb=" O VAL O 86 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL O 95 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL O 89 " --> pdb=" O LYS O 93 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS O 93 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA O 94 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU O 57 " --> pdb=" O VAL O 53 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL O 53 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE O 59 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE N 54 " --> pdb=" O GLN N 65 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN N 65 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL N 28 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL N 24 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR N 30 " --> pdb=" O HIS N 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU N 80 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU N 42 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU N 41 " --> pdb=" O ILE N 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 87 through 90 Processing sheet with id=AC5, first strand: chain 'N' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 98 through 99 current: chain 'N' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 309 through 312 current: chain 'N' and resid 401 through 408 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'N' and resid 135 through 137 removed outlier: 3.621A pdb=" N GLY N 154 " --> pdb=" O ILE N 166 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 146 through 147 removed outlier: 6.509A pdb=" N GLU N 193 " --> pdb=" O THR N 177 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 295 through 297 Processing sheet with id=AC9, first strand: chain 'N' and resid 431 through 432 Processing sheet with id=AD1, first strand: chain 'Q' and resid 120 through 123 removed outlier: 3.787A pdb=" N VAL Q 123 " --> pdb=" O ASP Q 149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP Q 149 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 131 through 132 removed outlier: 8.892A pdb=" N CYS Q 258 " --> pdb=" O PHE Q 227 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE Q 229 " --> pdb=" O CYS Q 258 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE Q 260 " --> pdb=" O ILE Q 229 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE Q 231 " --> pdb=" O PHE Q 260 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN Q 262 " --> pdb=" O PHE Q 231 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA Q 233 " --> pdb=" O ASN Q 262 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL Q 293 " --> pdb=" O THR Q 349 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE Q 351 " --> pdb=" O VAL Q 293 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL Q 295 " --> pdb=" O ILE Q 351 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 163 through 164 removed outlier: 4.289A pdb=" N ARG Q 340 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 169 through 170 removed outlier: 4.422A pdb=" N ILE Q 183 " --> pdb=" O ILE Q 170 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 375 through 376 Processing sheet with id=AD6, first strand: chain 'O' and resid 120 through 123 Processing sheet with id=AD7, first strand: chain 'O' and resid 131 through 133 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 131 through 133 current: chain 'O' and resid 257 through 263 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 257 through 263 current: chain 'O' and resid 347 through 355 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'O' and resid 169 through 170 removed outlier: 4.657A pdb=" N ILE O 183 " --> pdb=" O ILE O 170 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 375 through 376 Processing sheet with id=AE1, first strand: chain 'P' and resid 120 through 123 removed outlier: 3.515A pdb=" N ASP P 149 " --> pdb=" O VAL P 123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 131 through 133 removed outlier: 6.715A pdb=" N PHE P 132 " --> pdb=" O LEU P 261 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU P 263 " --> pdb=" O PHE P 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET P 234 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL P 293 " --> pdb=" O THR P 349 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE P 351 " --> pdb=" O VAL P 293 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL P 295 " --> pdb=" O ILE P 351 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY P 346 " --> pdb=" O VAL P 341 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL P 341 " --> pdb=" O GLY P 346 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG P 340 " --> pdb=" O ILE P 164 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE P 164 " --> pdb=" O ARG P 340 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 169 through 170 removed outlier: 4.504A pdb=" N ILE P 183 " --> pdb=" O ILE P 170 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 191 through 192 Processing sheet with id=AE5, first strand: chain 'c' and resid 164 through 167 1199 hydrogen bonds defined for protein. 3435 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: 13.21 Time building geometry restraints manager: 14.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11615 1.34 - 1.46: 6288 1.46 - 1.58: 18605 1.58 - 1.70: 0 1.70 - 1.82: 346 Bond restraints: 36854 Sorted by residual: bond pdb=" C ARG U 263 " pdb=" N HIS U 264 " ideal model delta sigma weight residual 1.333 1.390 -0.056 1.43e-02 4.89e+03 1.55e+01 bond pdb=" C TYR Q 504 " pdb=" N PRO Q 505 " ideal model delta sigma weight residual 1.333 1.376 -0.043 1.17e-02 7.31e+03 1.36e+01 bond pdb=" C HIS U 380 " pdb=" N SER U 381 " ideal model delta sigma weight residual 1.333 1.291 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C TYR O 504 " pdb=" N PRO O 505 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.97e+00 bond pdb=" CB VAL M 24 " pdb=" CG2 VAL M 24 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.27e+00 ... (remaining 36849 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.29: 806 105.29 - 112.53: 18280 112.53 - 119.78: 13765 119.78 - 127.03: 16660 127.03 - 134.28: 329 Bond angle restraints: 49840 Sorted by residual: angle pdb=" C ALA c 151 " pdb=" N ILE c 152 " pdb=" CA ILE c 152 " ideal model delta sigma weight residual 120.24 125.26 -5.02 6.30e-01 2.52e+00 6.36e+01 angle pdb=" C PHE N 472 " pdb=" N VAL N 473 " pdb=" CA VAL N 473 " ideal model delta sigma weight residual 120.24 124.45 -4.21 6.30e-01 2.52e+00 4.46e+01 angle pdb=" CA LEU M 234 " pdb=" CB LEU M 234 " pdb=" CG LEU M 234 " ideal model delta sigma weight residual 116.30 133.96 -17.66 3.50e+00 8.16e-02 2.55e+01 angle pdb=" C LYS c 107 " pdb=" N ASP c 108 " pdb=" CA ASP c 108 " ideal model delta sigma weight residual 121.54 131.12 -9.58 1.91e+00 2.74e-01 2.52e+01 angle pdb=" CA LEU L 234 " pdb=" CB LEU L 234 " pdb=" CG LEU L 234 " ideal model delta sigma weight residual 116.30 133.85 -17.55 3.50e+00 8.16e-02 2.52e+01 ... (remaining 49835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 19896 17.97 - 35.93: 2178 35.93 - 53.90: 358 53.90 - 71.86: 80 71.86 - 89.83: 38 Dihedral angle restraints: 22550 sinusoidal: 9067 harmonic: 13483 Sorted by residual: dihedral pdb=" CA TYR b 57 " pdb=" C TYR b 57 " pdb=" N GLU b 58 " pdb=" CA GLU b 58 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA PHE N 445 " pdb=" C PHE N 445 " pdb=" N PRO N 446 " pdb=" CA PRO N 446 " ideal model delta harmonic sigma weight residual 0.00 28.44 -28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA GLU d 29 " pdb=" C GLU d 29 " pdb=" N ILE d 30 " pdb=" CA ILE d 30 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 22547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4708 0.075 - 0.150: 834 0.150 - 0.225: 66 0.225 - 0.301: 7 0.301 - 0.376: 1 Chirality restraints: 5616 Sorted by residual: chirality pdb=" CB VAL O 213 " pdb=" CA VAL O 213 " pdb=" CG1 VAL O 213 " pdb=" CG2 VAL O 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB VAL P 213 " pdb=" CA VAL P 213 " pdb=" CG1 VAL P 213 " pdb=" CG2 VAL P 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE O 59 " pdb=" CA ILE O 59 " pdb=" CG1 ILE O 59 " pdb=" CG2 ILE O 59 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 5613 not shown) Planarity restraints: 6505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL Q 317 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO Q 318 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO Q 318 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Q 318 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET c 208 " -0.049 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO c 209 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO c 209 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO c 209 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET d 208 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO d 209 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO d 209 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO d 209 " -0.041 5.00e-02 4.00e+02 ... (remaining 6502 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 8634 2.78 - 3.31: 30776 3.31 - 3.84: 58924 3.84 - 4.37: 71290 4.37 - 4.90: 121158 Nonbonded interactions: 290782 Sorted by model distance: nonbonded pdb=" OH TYR Q 287 " pdb=" O GLY Q 339 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR c 112 " pdb=" OD2 ASP c 140 " model vdw 2.262 2.440 nonbonded pdb=" O GLY P 55 " pdb=" OG1 THR P 102 " model vdw 2.284 2.440 nonbonded pdb=" O LEU O 395 " pdb=" OH TYR O 423 " model vdw 2.285 2.440 nonbonded pdb=" OH TYR O 303 " pdb=" OD2 ASP O 330 " model vdw 2.289 2.440 ... (remaining 290777 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 'L' and (resid 17 through 248 or resid 257 through 616)) selection = (chain 'M' and (resid 17 through 248 or resid 257 through 616)) selection = (chain 'N' and (resid 17 through 248 or resid 257 through 616)) } ncs_group { reference = (chain 'O' and (resid 39 through 213 or resid 227 through 506)) selection = chain 'P' selection = (chain 'Q' and (resid 39 through 213 or resid 227 through 506)) } ncs_group { reference = (chain 'b' and ((resid 45 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 226)) selection = (chain 'c' and resid 45 through 226) } ncs_group { reference = (chain 'e' and ((resid 39 through 72 and (name N or name CA or name C or name O \ or name CB )) or resid 73 through 113)) selection = (chain 'f' and resid 39 through 113) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 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: 0.040 Extract box with map and model: 25.660 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 92.190 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.007 0.074 36854 Z= 0.489 Angle : 0.965 17.664 49840 Z= 0.554 Chirality : 0.057 0.376 5616 Planarity : 0.007 0.083 6505 Dihedral : 15.557 89.827 13874 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.47 % Allowed : 9.65 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -5.40 (0.09), residues: 4623 helix: -4.62 (0.05), residues: 1899 sheet: -2.51 (0.19), residues: 622 loop : -2.74 (0.11), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP L 450 HIS 0.010 0.002 HIS U 445 PHE 0.026 0.003 PHE L 291 TYR 0.021 0.002 TYR O 378 ARG 0.024 0.001 ARG Q 321 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 771 time to evaluate : 3.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 151 ASP cc_start: 0.7542 (m-30) cc_final: 0.7192 (m-30) REVERT: L 200 LYS cc_start: 0.5867 (ttmt) cc_final: 0.5336 (pttm) REVERT: L 235 ASP cc_start: 0.7934 (m-30) cc_final: 0.7644 (m-30) REVERT: L 484 GLN cc_start: 0.5769 (tp-100) cc_final: 0.5161 (tt0) REVERT: L 540 MET cc_start: 0.8320 (mtp) cc_final: 0.7605 (mtp) REVERT: L 604 LEU cc_start: 0.5764 (tp) cc_final: 0.5493 (tp) REVERT: D 13 ARG cc_start: 0.7023 (tpt90) cc_final: 0.6477 (tpt170) REVERT: D 34 LYS cc_start: 0.7374 (tptm) cc_final: 0.6914 (mmmt) REVERT: D 56 MET cc_start: 0.4721 (mmt) cc_final: 0.4249 (ppp) REVERT: D 140 LYS cc_start: 0.4599 (pttt) cc_final: 0.4372 (ttmm) REVERT: U 70 MET cc_start: 0.3352 (ttp) cc_final: 0.2983 (tpp) REVERT: U 72 ARG cc_start: 0.3263 (mtt90) cc_final: 0.2761 (ttm110) REVERT: U 124 ARG cc_start: 0.5832 (ttt180) cc_final: 0.5413 (ttt-90) REVERT: U 243 GLU cc_start: 0.3652 (pp20) cc_final: 0.3354 (mt-10) REVERT: U 333 MET cc_start: 0.7658 (mtt) cc_final: 0.7352 (mtt) REVERT: d 20 GLU cc_start: 0.5412 (mm-30) cc_final: 0.5147 (mm-30) REVERT: d 70 ILE cc_start: 0.8353 (mm) cc_final: 0.7928 (mt) REVERT: d 111 ARG cc_start: 0.6306 (ttp-110) cc_final: 0.5678 (mtp180) REVERT: M 314 ASN cc_start: 0.7610 (t0) cc_final: 0.7264 (t0) REVERT: M 478 LYS cc_start: 0.8091 (tppt) cc_final: 0.7505 (ttmt) REVERT: M 481 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6747 (tm-30) REVERT: M 494 GLN cc_start: 0.7471 (mt0) cc_final: 0.7219 (mt0) REVERT: M 521 GLN cc_start: 0.7665 (tt0) cc_final: 0.7360 (tt0) REVERT: M 523 ASN cc_start: 0.7890 (p0) cc_final: 0.7628 (p0) REVERT: N 129 ARG cc_start: 0.6690 (mmt90) cc_final: 0.6483 (mmt180) REVERT: N 163 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7217 (mttp) REVERT: N 289 ARG cc_start: 0.6213 (ttp-170) cc_final: 0.5277 (mmm160) REVERT: N 441 GLN cc_start: 0.5860 (mp10) cc_final: 0.5445 (mm-40) REVERT: N 517 ASP cc_start: 0.5810 (p0) cc_final: 0.5147 (p0) REVERT: N 525 TYR cc_start: 0.5461 (m-80) cc_final: 0.4775 (m-10) REVERT: N 547 PHE cc_start: 0.7416 (t80) cc_final: 0.7177 (t80) REVERT: N 550 MET cc_start: 0.5993 (mtm) cc_final: 0.5661 (mtm) REVERT: N 571 ARG cc_start: 0.6071 (ptt180) cc_final: 0.5666 (tmt-80) REVERT: Q 95 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8401 (t) REVERT: Q 117 ASP cc_start: 0.7600 (t0) cc_final: 0.7359 (t0) REVERT: Q 161 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7574 (tp-100) REVERT: Q 376 GLN cc_start: 0.7859 (mp10) cc_final: 0.7583 (mp10) REVERT: O 85 GLN cc_start: 0.8774 (tt0) cc_final: 0.8527 (tt0) REVERT: O 87 LEU cc_start: 0.8388 (tp) cc_final: 0.8183 (tp) REVERT: O 254 MET cc_start: 0.8593 (tpp) cc_final: 0.8385 (tpt) REVERT: O 402 MET cc_start: 0.8478 (ttt) cc_final: 0.7979 (ttt) REVERT: O 435 MET cc_start: 0.7336 (tpt) cc_final: 0.6767 (tpt) REVERT: O 497 GLN cc_start: 0.6262 (tp-100) cc_final: 0.6055 (mm110) REVERT: P 61 ASP cc_start: 0.6938 (t70) cc_final: 0.6635 (t0) REVERT: P 141 ARG cc_start: 0.6924 (mtm180) cc_final: 0.6422 (mmm-85) REVERT: P 249 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7188 (mt-10) REVERT: P 300 MET cc_start: 0.8842 (mmm) cc_final: 0.8624 (tpp) REVERT: P 421 GLN cc_start: 0.8297 (tp-100) cc_final: 0.8079 (tp-100) REVERT: P 456 GLN cc_start: 0.7132 (mm-40) cc_final: 0.6388 (mp10) REVERT: P 491 MET cc_start: 0.7287 (mtp) cc_final: 0.7014 (mtp) REVERT: b 141 PHE cc_start: 0.7987 (t80) cc_final: 0.7688 (t80) REVERT: c 59 LYS cc_start: 0.7697 (tptt) cc_final: 0.7392 (tptt) REVERT: c 65 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6371 (tm-30) REVERT: c 201 ASP cc_start: 0.8197 (m-30) cc_final: 0.7950 (m-30) REVERT: c 219 ASN cc_start: 0.7426 (t0) cc_final: 0.7007 (t0) REVERT: g 75 GLN cc_start: 0.5436 (pp30) cc_final: 0.4765 (mm-40) REVERT: g 88 GLN cc_start: 0.6678 (tm-30) cc_final: 0.6383 (tm-30) REVERT: e 93 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6560 (mp0) outliers start: 18 outliers final: 10 residues processed: 785 average time/residue: 0.5558 time to fit residues: 663.2929 Evaluate side-chains 537 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 526 time to evaluate : 4.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain P residue 365 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 388 optimal weight: 0.9990 chunk 348 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 360 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 417 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 172 ASN L 231 GLN L 441 GLN D 91 GLN D 137 ASN D 152 GLN U 145 GLN U 257 GLN U 349 ASN ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN ** U 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN d 78 GLN d 100 GLN d 139 GLN M 65 GLN M 123 ASN M 314 ASN M 430 GLN M 468 HIS M 494 GLN N 65 GLN N 242 GLN N 268 ASN N 430 GLN N 449 ASN ** N 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 573 HIS Q 97 GLN Q 199 HIS Q 256 ASN ** Q 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 HIS O 262 ASN O 288 GLN O 292 HIS O 385 ASN O 433 GLN O 456 GLN P 199 HIS P 256 ASN P 421 GLN b 78 GLN b 206 GLN c 113 GLN g 89 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36854 Z= 0.180 Angle : 0.587 13.266 49840 Z= 0.310 Chirality : 0.044 0.253 5616 Planarity : 0.005 0.062 6505 Dihedral : 5.869 71.633 5104 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.86 % Allowed : 14.12 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -4.12 (0.10), residues: 4623 helix: -3.12 (0.09), residues: 1958 sheet: -2.03 (0.19), residues: 640 loop : -2.39 (0.12), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 450 HIS 0.009 0.001 HIS d 14 PHE 0.020 0.001 PHE L 612 TYR 0.016 0.001 TYR L 601 ARG 0.032 0.000 ARG g 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 594 time to evaluate : 3.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 151 ASP cc_start: 0.7378 (m-30) cc_final: 0.7107 (m-30) REVERT: L 200 LYS cc_start: 0.5979 (ttmt) cc_final: 0.5524 (pttm) REVERT: L 235 ASP cc_start: 0.7915 (m-30) cc_final: 0.7613 (m-30) REVERT: L 284 MET cc_start: 0.7075 (tpp) cc_final: 0.6740 (tpt) REVERT: L 458 MET cc_start: 0.7439 (mtt) cc_final: 0.7206 (mtt) REVERT: L 484 GLN cc_start: 0.5913 (tp-100) cc_final: 0.5592 (tp40) REVERT: L 574 MET cc_start: 0.4587 (mtm) cc_final: 0.4299 (mtm) REVERT: L 586 PHE cc_start: 0.5813 (m-80) cc_final: 0.5477 (m-80) REVERT: D 10 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: D 34 LYS cc_start: 0.7367 (tptm) cc_final: 0.6893 (tttp) REVERT: U 72 ARG cc_start: 0.2841 (mtt90) cc_final: 0.2553 (ttm110) REVERT: U 111 MET cc_start: 0.5199 (mtm) cc_final: 0.4975 (mtt) REVERT: U 124 ARG cc_start: 0.5823 (ttt180) cc_final: 0.5502 (ttt-90) REVERT: U 173 MET cc_start: 0.3335 (mmt) cc_final: 0.2862 (mmt) REVERT: U 243 GLU cc_start: 0.3961 (pp20) cc_final: 0.3517 (mt-10) REVERT: d 20 GLU cc_start: 0.5175 (mm-30) cc_final: 0.4923 (mm-30) REVERT: d 47 GLN cc_start: 0.6674 (mp10) cc_final: 0.6420 (mp10) REVERT: d 70 ILE cc_start: 0.8103 (mm) cc_final: 0.7766 (mt) REVERT: d 111 ARG cc_start: 0.6387 (ttp-110) cc_final: 0.5798 (mtp180) REVERT: M 314 ASN cc_start: 0.7491 (t0) cc_final: 0.6969 (t0) REVERT: M 344 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.8029 (t) REVERT: M 478 LYS cc_start: 0.8151 (tppt) cc_final: 0.7897 (ttmt) REVERT: M 494 GLN cc_start: 0.7655 (mt0) cc_final: 0.7297 (tt0) REVERT: M 513 LYS cc_start: 0.8270 (tmtt) cc_final: 0.7467 (ttmt) REVERT: M 523 ASN cc_start: 0.7956 (p0) cc_final: 0.7619 (p0) REVERT: N 42 LEU cc_start: 0.8368 (mt) cc_final: 0.8032 (mt) REVERT: N 163 LYS cc_start: 0.7509 (mmtt) cc_final: 0.7106 (mttp) REVERT: N 289 ARG cc_start: 0.6176 (ttp-170) cc_final: 0.5974 (ttp-170) REVERT: N 515 ILE cc_start: 0.6624 (mt) cc_final: 0.6361 (mm) REVERT: N 525 TYR cc_start: 0.5378 (m-80) cc_final: 0.4372 (p90) REVERT: N 571 ARG cc_start: 0.6121 (ptt180) cc_final: 0.5920 (tmt-80) REVERT: Q 161 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7563 (tp40) REVERT: Q 249 GLU cc_start: 0.5840 (pt0) cc_final: 0.5593 (mt-10) REVERT: Q 446 SER cc_start: 0.7489 (m) cc_final: 0.7171 (p) REVERT: Q 460 ARG cc_start: 0.7298 (mmt180) cc_final: 0.6595 (mtp-110) REVERT: O 87 LEU cc_start: 0.8579 (tp) cc_final: 0.8316 (tp) REVERT: O 88 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7439 (tm-30) REVERT: O 387 GLN cc_start: 0.7492 (mp10) cc_final: 0.7038 (mp10) REVERT: O 402 MET cc_start: 0.8348 (ttt) cc_final: 0.7850 (ttt) REVERT: P 61 ASP cc_start: 0.6974 (t70) cc_final: 0.6750 (t0) REVERT: P 141 ARG cc_start: 0.6862 (mtm180) cc_final: 0.6422 (mmm-85) REVERT: P 300 MET cc_start: 0.8922 (mmm) cc_final: 0.8713 (tpp) REVERT: P 359 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: P 402 MET cc_start: 0.8069 (ttt) cc_final: 0.7798 (ttp) REVERT: P 456 GLN cc_start: 0.6976 (mm-40) cc_final: 0.5811 (mp10) REVERT: c 59 LYS cc_start: 0.7584 (tptt) cc_final: 0.7361 (tptt) REVERT: c 219 ASN cc_start: 0.7427 (t0) cc_final: 0.7038 (t0) REVERT: e 93 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6484 (mp0) REVERT: f 92 ARG cc_start: 0.8209 (ptt180) cc_final: 0.7938 (ttp-170) outliers start: 72 outliers final: 33 residues processed: 641 average time/residue: 0.5147 time to fit residues: 523.2720 Evaluate side-chains 538 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 502 time to evaluate : 4.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 391 ASN Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 517 ASP Chi-restraints excluded: chain N residue 268 ASN Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 523 ASN Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain P residue 359 ASP Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 109 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 232 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 284 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 418 optimal weight: 40.0000 chunk 452 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 414 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 335 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 449 ASN U 85 ASN ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 221 ASN N 164 HIS N 449 ASN ** N 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 HIS ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 363 HIS ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS P 421 GLN b 71 GLN ** c 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 36854 Z= 0.462 Angle : 0.736 15.121 49840 Z= 0.380 Chirality : 0.050 0.242 5616 Planarity : 0.006 0.069 6505 Dihedral : 6.204 75.547 5095 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.78 % Allowed : 17.49 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -3.66 (0.11), residues: 4623 helix: -2.43 (0.10), residues: 1949 sheet: -1.95 (0.20), residues: 614 loop : -2.46 (0.12), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP U 199 HIS 0.011 0.002 HIS U 445 PHE 0.022 0.002 PHE M 469 TYR 0.026 0.002 TYR c 112 ARG 0.013 0.001 ARG b 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 502 time to evaluate : 4.158 Fit side-chains revert: symmetry clash REVERT: L 200 LYS cc_start: 0.6038 (ttmt) cc_final: 0.5561 (pttm) REVERT: L 235 ASP cc_start: 0.7991 (m-30) cc_final: 0.7598 (m-30) REVERT: L 458 MET cc_start: 0.7415 (mtt) cc_final: 0.7177 (mtt) REVERT: L 484 GLN cc_start: 0.6034 (tp-100) cc_final: 0.5659 (tp40) REVERT: L 574 MET cc_start: 0.4739 (mtm) cc_final: 0.4521 (mtm) REVERT: L 579 TYR cc_start: 0.7030 (t80) cc_final: 0.6577 (t80) REVERT: D 10 PHE cc_start: 0.6791 (t80) cc_final: 0.6272 (m-80) REVERT: D 34 LYS cc_start: 0.7457 (tptm) cc_final: 0.7030 (tttp) REVERT: D 62 MET cc_start: 0.5043 (mtt) cc_final: 0.4598 (mmm) REVERT: D 214 GLU cc_start: 0.3547 (tp30) cc_final: 0.3092 (tt0) REVERT: U 72 ARG cc_start: 0.2903 (mtt90) cc_final: 0.2689 (ttm110) REVERT: U 124 ARG cc_start: 0.5906 (ttt180) cc_final: 0.5542 (ttt-90) REVERT: U 199 TRP cc_start: 0.6114 (t60) cc_final: 0.5328 (t60) REVERT: U 243 GLU cc_start: 0.3586 (pp20) cc_final: 0.3043 (mt-10) REVERT: U 253 TYR cc_start: 0.7138 (t80) cc_final: 0.6866 (t80) REVERT: U 333 MET cc_start: 0.7635 (mtt) cc_final: 0.7392 (mtt) REVERT: d 20 GLU cc_start: 0.5278 (mm-30) cc_final: 0.4964 (mm-30) REVERT: d 68 LYS cc_start: 0.6815 (mttm) cc_final: 0.6486 (tttm) REVERT: d 70 ILE cc_start: 0.8265 (mm) cc_final: 0.7984 (mt) REVERT: d 111 ARG cc_start: 0.6510 (ttp-110) cc_final: 0.6000 (mtp180) REVERT: d 155 TYR cc_start: 0.8609 (t80) cc_final: 0.8409 (t80) REVERT: M 234 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7785 (pt) REVERT: M 314 ASN cc_start: 0.7872 (t0) cc_final: 0.7513 (t0) REVERT: M 347 MET cc_start: 0.7874 (tpp) cc_final: 0.7664 (tpp) REVERT: M 353 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7820 (mtt90) REVERT: M 505 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7138 (t70) REVERT: M 523 ASN cc_start: 0.8075 (p0) cc_final: 0.7523 (p0) REVERT: N 163 LYS cc_start: 0.7455 (mmtt) cc_final: 0.7063 (mttp) REVERT: N 289 ARG cc_start: 0.6173 (ttp-170) cc_final: 0.5951 (ttp-170) REVERT: N 515 ILE cc_start: 0.6589 (mt) cc_final: 0.6335 (mm) REVERT: N 547 PHE cc_start: 0.7147 (t80) cc_final: 0.6866 (t80) REVERT: Q 61 ASP cc_start: 0.7498 (t0) cc_final: 0.7216 (t70) REVERT: Q 161 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7647 (tp-100) REVERT: Q 360 ASP cc_start: 0.7204 (p0) cc_final: 0.6891 (p0) REVERT: Q 446 SER cc_start: 0.7718 (m) cc_final: 0.7474 (p) REVERT: O 88 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7956 (tp30) REVERT: O 309 GLU cc_start: 0.7642 (tt0) cc_final: 0.7441 (tt0) REVERT: O 482 GLN cc_start: 0.7851 (pt0) cc_final: 0.7633 (mt0) REVERT: P 61 ASP cc_start: 0.6929 (t70) cc_final: 0.6620 (t0) REVERT: P 456 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6459 (mp10) REVERT: c 93 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: c 219 ASN cc_start: 0.7434 (t0) cc_final: 0.7014 (t0) REVERT: e 93 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6436 (mp0) REVERT: e 109 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6224 (tt0) outliers start: 146 outliers final: 103 residues processed: 616 average time/residue: 0.4974 time to fit residues: 488.0675 Evaluate side-chains 575 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 468 time to evaluate : 4.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 518 ASP Chi-restraints excluded: chain L residue 525 TYR Chi-restraints excluded: chain L residue 592 ASP Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain U residue 31 LEU Chi-restraints excluded: chain U residue 62 MET Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 282 LEU Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain d residue 162 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 505 ASP Chi-restraints excluded: chain M residue 529 ASP Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 493 VAL Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain N residue 523 ASN Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain Q residue 371 TYR Chi-restraints excluded: chain Q residue 445 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 177 ILE Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 127 MET Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 177 ILE Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 109 GLN Chi-restraints excluded: chain f residue 102 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 419 optimal weight: 6.9990 chunk 444 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 398 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN U 163 GLN ** U 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 ASN ** N 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 433 GLN O 456 GLN c 77 ASN c 206 GLN f 85 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36854 Z= 0.169 Angle : 0.543 13.752 49840 Z= 0.282 Chirality : 0.043 0.267 5616 Planarity : 0.004 0.063 6505 Dihedral : 5.391 74.631 5095 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.33 % Allowed : 19.71 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.94 (0.11), residues: 4623 helix: -1.70 (0.11), residues: 1947 sheet: -1.66 (0.20), residues: 618 loop : -2.19 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 199 HIS 0.008 0.001 HIS U 205 PHE 0.015 0.001 PHE M 469 TYR 0.019 0.001 TYR D 119 ARG 0.007 0.000 ARG N 553 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 518 time to evaluate : 4.378 Fit side-chains REVERT: L 200 LYS cc_start: 0.5972 (ttmt) cc_final: 0.5528 (pttm) REVERT: L 235 ASP cc_start: 0.8007 (m-30) cc_final: 0.7767 (m-30) REVERT: L 484 GLN cc_start: 0.6188 (tp-100) cc_final: 0.5713 (tp40) REVERT: L 516 LYS cc_start: 0.7288 (mttt) cc_final: 0.7019 (mttt) REVERT: L 540 MET cc_start: 0.8019 (mtp) cc_final: 0.7776 (mtp) REVERT: L 574 MET cc_start: 0.4709 (mtm) cc_final: 0.4438 (mtm) REVERT: L 596 LYS cc_start: 0.6378 (mtmm) cc_final: 0.5955 (tptp) REVERT: D 10 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.6119 (m-80) REVERT: D 62 MET cc_start: 0.5042 (mtt) cc_final: 0.4670 (mmm) REVERT: D 214 GLU cc_start: 0.3561 (tp30) cc_final: 0.3158 (tt0) REVERT: U 124 ARG cc_start: 0.5987 (ttt180) cc_final: 0.5635 (ttt-90) REVERT: U 243 GLU cc_start: 0.3552 (pp20) cc_final: 0.3170 (mt-10) REVERT: U 432 GLU cc_start: 0.6289 (mp0) cc_final: 0.5963 (mp0) REVERT: d 20 GLU cc_start: 0.5161 (mm-30) cc_final: 0.4957 (mm-30) REVERT: d 68 LYS cc_start: 0.6785 (mttm) cc_final: 0.6490 (tttm) REVERT: d 70 ILE cc_start: 0.8180 (mm) cc_final: 0.7827 (mt) REVERT: d 85 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7543 (mtm-85) REVERT: d 111 ARG cc_start: 0.6488 (ttp-110) cc_final: 0.5919 (mtp180) REVERT: M 314 ASN cc_start: 0.7633 (t0) cc_final: 0.7183 (t0) REVERT: M 426 LEU cc_start: 0.8536 (mm) cc_final: 0.8282 (mp) REVERT: M 478 LYS cc_start: 0.8256 (tppt) cc_final: 0.7884 (ttmt) REVERT: M 494 GLN cc_start: 0.7814 (mt0) cc_final: 0.7548 (tt0) REVERT: M 505 ASP cc_start: 0.7233 (t0) cc_final: 0.7024 (t70) REVERT: N 163 LYS cc_start: 0.7418 (mmtt) cc_final: 0.7047 (mttp) REVERT: N 289 ARG cc_start: 0.6166 (ttp-170) cc_final: 0.5907 (ttp-170) REVERT: N 517 ASP cc_start: 0.5599 (p0) cc_final: 0.5386 (t70) REVERT: N 544 MET cc_start: 0.6139 (mtp) cc_final: 0.5878 (mtp) REVERT: Q 161 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7443 (tp-100) REVERT: Q 314 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.6004 (ttt90) REVERT: O 88 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7562 (tm-30) REVERT: O 435 MET cc_start: 0.7724 (tpt) cc_final: 0.7270 (tpp) REVERT: P 61 ASP cc_start: 0.6896 (t70) cc_final: 0.6653 (t0) REVERT: P 402 MET cc_start: 0.8068 (ttt) cc_final: 0.7847 (ttp) REVERT: P 456 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6425 (mp10) REVERT: b 111 ARG cc_start: 0.7450 (mtp180) cc_final: 0.7204 (mtp-110) REVERT: c 59 LYS cc_start: 0.7534 (tptt) cc_final: 0.7267 (tptt) REVERT: c 197 GLU cc_start: 0.7943 (mp0) cc_final: 0.7512 (mt-10) REVERT: c 219 ASN cc_start: 0.7358 (t0) cc_final: 0.6915 (t0) REVERT: g 78 ARG cc_start: 0.5027 (ptp90) cc_final: 0.4761 (ptp90) REVERT: e 93 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6398 (mp0) outliers start: 90 outliers final: 56 residues processed: 583 average time/residue: 0.5148 time to fit residues: 480.2593 Evaluate side-chains 533 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 475 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 529 ASP Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 523 ASN Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 314 ARG Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 501 SER Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 177 ILE Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 104 CYS Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 370 optimal weight: 8.9990 chunk 252 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 379 optimal weight: 4.9990 chunk 307 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 399 optimal weight: 0.2980 chunk 112 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 350 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN ** U 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 ASN ** N 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 262 ASN b 71 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36854 Z= 0.195 Angle : 0.537 12.437 49840 Z= 0.277 Chirality : 0.044 0.273 5616 Planarity : 0.004 0.065 6505 Dihedral : 5.172 74.765 5095 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.10 % Allowed : 19.53 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.48 (0.12), residues: 4623 helix: -1.26 (0.11), residues: 1954 sheet: -1.44 (0.21), residues: 608 loop : -1.99 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 450 HIS 0.005 0.001 HIS U 97 PHE 0.014 0.001 PHE M 337 TYR 0.020 0.001 TYR P 423 ARG 0.007 0.000 ARG N 553 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 507 time to evaluate : 4.118 Fit side-chains revert: symmetry clash REVERT: L 151 ASP cc_start: 0.7375 (m-30) cc_final: 0.7130 (m-30) REVERT: L 200 LYS cc_start: 0.5940 (ttmt) cc_final: 0.5456 (pttm) REVERT: L 235 ASP cc_start: 0.8011 (m-30) cc_final: 0.7743 (m-30) REVERT: L 284 MET cc_start: 0.6873 (tpp) cc_final: 0.6637 (tpp) REVERT: L 484 GLN cc_start: 0.6222 (tp-100) cc_final: 0.5657 (tp40) REVERT: L 516 LYS cc_start: 0.7281 (mttt) cc_final: 0.7058 (mttt) REVERT: L 574 MET cc_start: 0.4677 (mtm) cc_final: 0.4457 (mtm) REVERT: L 596 LYS cc_start: 0.6358 (mtmm) cc_final: 0.5895 (tptp) REVERT: L 605 LEU cc_start: 0.7054 (tp) cc_final: 0.6833 (tp) REVERT: D 10 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5977 (m-80) REVERT: D 62 MET cc_start: 0.5071 (mtt) cc_final: 0.4758 (mmm) REVERT: U 95 MET cc_start: 0.3842 (mmp) cc_final: 0.2146 (ptp) REVERT: U 124 ARG cc_start: 0.6049 (ttt180) cc_final: 0.5694 (ttt-90) REVERT: U 199 TRP cc_start: 0.5923 (t60) cc_final: 0.5459 (t60) REVERT: U 243 GLU cc_start: 0.3458 (pp20) cc_final: 0.3004 (mt-10) REVERT: U 253 TYR cc_start: 0.6807 (t80) cc_final: 0.6447 (t80) REVERT: U 273 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: U 432 GLU cc_start: 0.6338 (mp0) cc_final: 0.5926 (mp0) REVERT: d 20 GLU cc_start: 0.5081 (mm-30) cc_final: 0.4844 (mm-30) REVERT: d 37 GLU cc_start: 0.7181 (tp30) cc_final: 0.6802 (tp30) REVERT: d 68 LYS cc_start: 0.6792 (mttm) cc_final: 0.6508 (tttm) REVERT: d 70 ILE cc_start: 0.8150 (mm) cc_final: 0.7808 (mt) REVERT: d 111 ARG cc_start: 0.6461 (ttp-110) cc_final: 0.5950 (mtp180) REVERT: M 74 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8277 (p) REVERT: M 234 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7647 (pt) REVERT: M 314 ASN cc_start: 0.7638 (t0) cc_final: 0.7189 (t0) REVERT: M 353 ARG cc_start: 0.8019 (mtt90) cc_final: 0.7797 (mtt90) REVERT: M 426 LEU cc_start: 0.8578 (mm) cc_final: 0.8321 (mp) REVERT: M 478 LYS cc_start: 0.8273 (tppt) cc_final: 0.7838 (ttmt) REVERT: M 494 GLN cc_start: 0.7867 (mt0) cc_final: 0.7631 (tt0) REVERT: N 129 ARG cc_start: 0.7003 (mpt180) cc_final: 0.6774 (mmt180) REVERT: N 163 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7075 (mttp) REVERT: N 289 ARG cc_start: 0.6183 (ttp-170) cc_final: 0.5900 (ttp-170) REVERT: Q 161 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7372 (tp-100) REVERT: O 88 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7601 (tm-30) REVERT: O 435 MET cc_start: 0.7717 (tpt) cc_final: 0.7462 (tpt) REVERT: P 61 ASP cc_start: 0.6915 (t70) cc_final: 0.6690 (t0) REVERT: P 402 MET cc_start: 0.8086 (ttt) cc_final: 0.7880 (ttp) REVERT: P 456 GLN cc_start: 0.7134 (mm-40) cc_final: 0.6425 (mp10) REVERT: b 111 ARG cc_start: 0.7460 (mtp180) cc_final: 0.7193 (mtp-110) REVERT: c 143 LEU cc_start: 0.7605 (mp) cc_final: 0.7265 (mp) REVERT: c 197 GLU cc_start: 0.7856 (mp0) cc_final: 0.7440 (mt-10) REVERT: c 219 ASN cc_start: 0.7385 (t0) cc_final: 0.6909 (t0) REVERT: e 93 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6387 (mp0) REVERT: e 109 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.6124 (tt0) outliers start: 120 outliers final: 82 residues processed: 595 average time/residue: 0.4994 time to fit residues: 473.8018 Evaluate side-chains 568 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 481 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 518 ASP Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 273 GLU Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 391 ASN Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 523 ASN Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 433 GLN Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain Q residue 445 THR Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 501 SER Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 237 ASN Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 109 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 7.9990 chunk 400 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 445 optimal weight: 4.9990 chunk 369 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 350 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 ASN ** N 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 209 GLN ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 36854 Z= 0.350 Angle : 0.632 13.045 49840 Z= 0.325 Chirality : 0.047 0.244 5616 Planarity : 0.005 0.062 6505 Dihedral : 5.578 75.954 5095 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.83 % Allowed : 20.23 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.55 (0.12), residues: 4623 helix: -1.31 (0.11), residues: 1957 sheet: -1.52 (0.21), residues: 591 loop : -2.04 (0.12), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 450 HIS 0.008 0.001 HIS d 14 PHE 0.018 0.002 PHE M 337 TYR 0.021 0.002 TYR P 423 ARG 0.004 0.001 ARG L 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 490 time to evaluate : 4.098 Fit side-chains REVERT: L 200 LYS cc_start: 0.5970 (ttmt) cc_final: 0.5532 (pttm) REVERT: L 235 ASP cc_start: 0.8007 (m-30) cc_final: 0.7536 (m-30) REVERT: L 484 GLN cc_start: 0.6273 (tp-100) cc_final: 0.5716 (tp40) REVERT: L 574 MET cc_start: 0.4858 (mtm) cc_final: 0.4634 (mtm) REVERT: L 579 TYR cc_start: 0.6993 (t80) cc_final: 0.6590 (t80) REVERT: L 596 LYS cc_start: 0.6577 (mtmm) cc_final: 0.6073 (tptp) REVERT: D 10 PHE cc_start: 0.6517 (t80) cc_final: 0.6042 (m-80) REVERT: D 62 MET cc_start: 0.5183 (mtt) cc_final: 0.4857 (mmm) REVERT: D 138 TYR cc_start: 0.4406 (OUTLIER) cc_final: 0.4189 (m-10) REVERT: U 109 MET cc_start: 0.4572 (mmt) cc_final: 0.3813 (mmm) REVERT: U 124 ARG cc_start: 0.5969 (ttt180) cc_final: 0.5598 (ttt-90) REVERT: U 199 TRP cc_start: 0.6349 (t60) cc_final: 0.5600 (t60) REVERT: U 273 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: d 8 VAL cc_start: 0.6121 (OUTLIER) cc_final: 0.5794 (t) REVERT: d 20 GLU cc_start: 0.5172 (mm-30) cc_final: 0.4952 (mm-30) REVERT: d 57 TYR cc_start: 0.7128 (m-80) cc_final: 0.6643 (m-10) REVERT: d 68 LYS cc_start: 0.6879 (mttm) cc_final: 0.6536 (tttm) REVERT: d 70 ILE cc_start: 0.8221 (mm) cc_final: 0.7926 (mt) REVERT: d 111 ARG cc_start: 0.6530 (ttp-110) cc_final: 0.6031 (mtp180) REVERT: d 184 TYR cc_start: 0.7353 (m-80) cc_final: 0.7090 (m-80) REVERT: M 234 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7679 (pt) REVERT: M 314 ASN cc_start: 0.7839 (t0) cc_final: 0.7470 (t0) REVERT: M 347 MET cc_start: 0.7858 (tpp) cc_final: 0.7592 (tpp) REVERT: M 426 LEU cc_start: 0.8617 (mm) cc_final: 0.8263 (mp) REVERT: N 95 MET cc_start: 0.7917 (mmp) cc_final: 0.7714 (mmp) REVERT: N 163 LYS cc_start: 0.7482 (mmtt) cc_final: 0.7074 (mttp) REVERT: N 289 ARG cc_start: 0.6214 (ttp-170) cc_final: 0.5966 (ttp-170) REVERT: N 450 TRP cc_start: 0.7070 (p90) cc_final: 0.6610 (p90) REVERT: N 550 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5909 (mtt) REVERT: Q 161 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7629 (tp-100) REVERT: O 88 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7801 (tm-30) REVERT: O 435 MET cc_start: 0.7678 (tpt) cc_final: 0.7381 (tpt) REVERT: O 456 GLN cc_start: 0.7383 (tt0) cc_final: 0.7115 (tp-100) REVERT: P 61 ASP cc_start: 0.6943 (t70) cc_final: 0.6702 (t0) REVERT: P 456 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6507 (mp10) REVERT: b 111 ARG cc_start: 0.7564 (mtp180) cc_final: 0.7255 (mtp-110) REVERT: c 197 GLU cc_start: 0.7932 (mp0) cc_final: 0.7508 (mt-10) REVERT: c 219 ASN cc_start: 0.7403 (t0) cc_final: 0.6982 (t0) REVERT: e 82 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7451 (mm-40) REVERT: e 93 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6820 (mp0) REVERT: e 109 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6066 (tt0) outliers start: 148 outliers final: 114 residues processed: 612 average time/residue: 0.4894 time to fit residues: 483.0139 Evaluate side-chains 593 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 473 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 518 ASP Chi-restraints excluded: chain L residue 525 TYR Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 273 GLU Chi-restraints excluded: chain U residue 282 LEU Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 452 VAL Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 162 ASP Chi-restraints excluded: chain d residue 168 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 164 HIS Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 493 VAL Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain N residue 523 ASN Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain Q residue 445 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 499 THR Chi-restraints excluded: chain O residue 501 SER Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 237 ASN Chi-restraints excluded: chain P residue 354 LEU Chi-restraints excluded: chain P residue 439 VAL Chi-restraints excluded: chain P residue 455 LEU Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 144 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 177 ILE Chi-restraints excluded: chain g residue 96 LEU Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 104 CYS Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 109 GLN Chi-restraints excluded: chain f residue 102 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 429 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 374 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 443 optimal weight: 5.9990 chunk 277 optimal weight: 8.9990 chunk 270 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 314 ASN U 350 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN ** U 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 317 ASN N 268 ASN ** N 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 205 GLN ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 36854 Z= 0.379 Angle : 0.651 12.789 49840 Z= 0.335 Chirality : 0.048 0.247 5616 Planarity : 0.005 0.062 6505 Dihedral : 5.704 75.747 5094 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.40 % Allowed : 20.41 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.54 (0.12), residues: 4623 helix: -1.26 (0.11), residues: 1947 sheet: -1.61 (0.21), residues: 597 loop : -2.04 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 433 HIS 0.008 0.001 HIS d 14 PHE 0.019 0.002 PHE M 337 TYR 0.021 0.002 TYR M 266 ARG 0.004 0.001 ARG U 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 487 time to evaluate : 4.296 Fit side-chains REVERT: L 151 ASP cc_start: 0.7496 (m-30) cc_final: 0.7113 (m-30) REVERT: L 200 LYS cc_start: 0.6046 (ttmt) cc_final: 0.5680 (pttm) REVERT: L 235 ASP cc_start: 0.8030 (m-30) cc_final: 0.7551 (m-30) REVERT: L 484 GLN cc_start: 0.6250 (tp-100) cc_final: 0.5690 (tp40) REVERT: L 556 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.4155 (tm-30) REVERT: L 574 MET cc_start: 0.4927 (mtm) cc_final: 0.4690 (mtm) REVERT: L 579 TYR cc_start: 0.7051 (t80) cc_final: 0.6632 (t80) REVERT: L 596 LYS cc_start: 0.6625 (mtmm) cc_final: 0.6104 (tptp) REVERT: D 10 PHE cc_start: 0.6676 (t80) cc_final: 0.6222 (m-80) REVERT: U 124 ARG cc_start: 0.5964 (ttt180) cc_final: 0.5610 (ttt-90) REVERT: U 199 TRP cc_start: 0.6039 (t60) cc_final: 0.5785 (t60) REVERT: d 20 GLU cc_start: 0.5156 (mm-30) cc_final: 0.4939 (mm-30) REVERT: d 37 GLU cc_start: 0.7327 (tp30) cc_final: 0.6986 (tp30) REVERT: d 68 LYS cc_start: 0.6905 (mttm) cc_final: 0.6554 (tttm) REVERT: d 70 ILE cc_start: 0.8274 (mm) cc_final: 0.7998 (mt) REVERT: d 111 ARG cc_start: 0.6594 (ttp-110) cc_final: 0.6111 (mtp180) REVERT: d 184 TYR cc_start: 0.7374 (m-80) cc_final: 0.7084 (m-80) REVERT: M 142 ARG cc_start: 0.6456 (ptp90) cc_final: 0.5692 (mtt180) REVERT: M 234 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7716 (pt) REVERT: M 314 ASN cc_start: 0.7890 (t0) cc_final: 0.7510 (t0) REVERT: M 353 ARG cc_start: 0.8030 (mtt90) cc_final: 0.7817 (mtt90) REVERT: M 426 LEU cc_start: 0.8639 (mm) cc_final: 0.8268 (mp) REVERT: M 523 ASN cc_start: 0.8108 (p0) cc_final: 0.7738 (p0) REVERT: N 141 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6304 (mp) REVERT: N 163 LYS cc_start: 0.7436 (mmtt) cc_final: 0.7018 (mttp) REVERT: N 450 TRP cc_start: 0.7085 (p90) cc_final: 0.6832 (p90) REVERT: N 550 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5664 (mtt) REVERT: N 597 ILE cc_start: 0.6397 (OUTLIER) cc_final: 0.6080 (mp) REVERT: Q 161 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7712 (tp-100) REVERT: O 88 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7829 (tm-30) REVERT: O 435 MET cc_start: 0.7702 (tpt) cc_final: 0.7384 (tpt) REVERT: O 456 GLN cc_start: 0.7390 (tt0) cc_final: 0.7104 (tp-100) REVERT: P 61 ASP cc_start: 0.6979 (t70) cc_final: 0.6749 (t0) REVERT: P 456 GLN cc_start: 0.7355 (mm-40) cc_final: 0.6574 (mp10) REVERT: b 111 ARG cc_start: 0.7567 (mtp180) cc_final: 0.7216 (mtp-110) REVERT: c 197 GLU cc_start: 0.7937 (mp0) cc_final: 0.7509 (mt-10) REVERT: c 219 ASN cc_start: 0.7357 (t0) cc_final: 0.6919 (t0) REVERT: g 72 GLU cc_start: 0.5954 (pp20) cc_final: 0.5229 (pp20) REVERT: e 93 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6886 (mp0) REVERT: e 109 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.6060 (tt0) outliers start: 170 outliers final: 136 residues processed: 629 average time/residue: 0.4841 time to fit residues: 491.1497 Evaluate side-chains 609 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 467 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 518 ASP Chi-restraints excluded: chain L residue 525 TYR Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 391 ASN Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 452 VAL Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 16 MET Chi-restraints excluded: chain d residue 63 GLN Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 162 ASP Chi-restraints excluded: chain d residue 168 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 164 HIS Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 552 ARG Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 268 ASN Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 493 VAL Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain N residue 523 ASN Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 597 ILE Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain Q residue 445 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 177 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 369 THR Chi-restraints excluded: chain O residue 499 THR Chi-restraints excluded: chain O residue 501 SER Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain P residue 237 ASN Chi-restraints excluded: chain P residue 354 LEU Chi-restraints excluded: chain P residue 439 VAL Chi-restraints excluded: chain P residue 455 LEU Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 144 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 177 ILE Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain g residue 104 CYS Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 109 GLN Chi-restraints excluded: chain f residue 82 GLN Chi-restraints excluded: chain f residue 84 MET Chi-restraints excluded: chain f residue 102 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 274 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 264 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 281 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 348 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN L 573 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN ** U 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 ASN ** N 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 205 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36854 Z= 0.176 Angle : 0.546 12.036 49840 Z= 0.282 Chirality : 0.044 0.279 5616 Planarity : 0.004 0.063 6505 Dihedral : 5.175 75.127 5094 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.92 % Allowed : 21.88 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.00 (0.12), residues: 4623 helix: -0.80 (0.12), residues: 1952 sheet: -1.19 (0.22), residues: 588 loop : -1.80 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 433 HIS 0.006 0.001 HIS U 97 PHE 0.013 0.001 PHE D 199 TYR 0.020 0.001 TYR P 423 ARG 0.005 0.000 ARG N 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 493 time to evaluate : 4.294 Fit side-chains REVERT: L 151 ASP cc_start: 0.7459 (m-30) cc_final: 0.7103 (m-30) REVERT: L 200 LYS cc_start: 0.5966 (ttmt) cc_final: 0.5698 (pttm) REVERT: L 235 ASP cc_start: 0.8021 (m-30) cc_final: 0.7815 (m-30) REVERT: L 484 GLN cc_start: 0.6201 (tp-100) cc_final: 0.5648 (tp40) REVERT: L 485 GLU cc_start: 0.6859 (tt0) cc_final: 0.5310 (mm-30) REVERT: L 556 GLU cc_start: 0.5337 (OUTLIER) cc_final: 0.4082 (tm-30) REVERT: L 596 LYS cc_start: 0.6457 (mtmm) cc_final: 0.5966 (tptp) REVERT: D 10 PHE cc_start: 0.6408 (t80) cc_final: 0.5926 (m-80) REVERT: D 56 MET cc_start: 0.5661 (tmm) cc_final: 0.5383 (tmm) REVERT: D 62 MET cc_start: 0.4449 (mmm) cc_final: 0.4230 (mmm) REVERT: D 119 TYR cc_start: 0.3246 (m-80) cc_final: 0.3011 (m-10) REVERT: U 95 MET cc_start: 0.3945 (mmp) cc_final: 0.2155 (ptp) REVERT: U 109 MET cc_start: 0.4584 (mmt) cc_final: 0.3854 (mmm) REVERT: U 124 ARG cc_start: 0.6045 (ttt180) cc_final: 0.5691 (ttt-90) REVERT: U 199 TRP cc_start: 0.6325 (t60) cc_final: 0.5564 (t60) REVERT: d 8 VAL cc_start: 0.6134 (OUTLIER) cc_final: 0.5833 (t) REVERT: d 37 GLU cc_start: 0.7220 (tp30) cc_final: 0.6882 (tp30) REVERT: d 57 TYR cc_start: 0.6921 (m-80) cc_final: 0.6453 (m-10) REVERT: d 68 LYS cc_start: 0.6780 (mttm) cc_final: 0.6535 (tttm) REVERT: d 111 ARG cc_start: 0.6458 (ttp-110) cc_final: 0.6052 (mtp180) REVERT: M 74 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8322 (p) REVERT: M 142 ARG cc_start: 0.6469 (ptp90) cc_final: 0.5746 (mtt180) REVERT: M 234 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7648 (pt) REVERT: M 314 ASN cc_start: 0.7750 (t0) cc_final: 0.7323 (t0) REVERT: M 426 LEU cc_start: 0.8610 (mm) cc_final: 0.8371 (mp) REVERT: M 478 LYS cc_start: 0.8296 (tppt) cc_final: 0.7829 (ttmt) REVERT: M 503 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6726 (mm-30) REVERT: M 523 ASN cc_start: 0.8061 (p0) cc_final: 0.7783 (p0) REVERT: N 163 LYS cc_start: 0.7367 (mmtt) cc_final: 0.7102 (mttp) REVERT: N 289 ARG cc_start: 0.5661 (ttp-170) cc_final: 0.5112 (mmm160) REVERT: N 550 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5606 (mtt) REVERT: Q 161 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7543 (tp-100) REVERT: Q 360 ASP cc_start: 0.7103 (p0) cc_final: 0.6543 (p0) REVERT: O 88 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7748 (tm-30) REVERT: O 435 MET cc_start: 0.7648 (tpt) cc_final: 0.7352 (tpp) REVERT: P 456 GLN cc_start: 0.7336 (mm-40) cc_final: 0.6528 (mp10) REVERT: b 111 ARG cc_start: 0.7483 (mtp180) cc_final: 0.7166 (mtp-110) REVERT: c 59 LYS cc_start: 0.7550 (tptt) cc_final: 0.7257 (tptt) REVERT: c 197 GLU cc_start: 0.7851 (mp0) cc_final: 0.7505 (mt-10) REVERT: c 201 ASP cc_start: 0.8051 (m-30) cc_final: 0.7837 (m-30) REVERT: c 219 ASN cc_start: 0.7421 (t0) cc_final: 0.6965 (t0) REVERT: c 225 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6429 (tp) REVERT: g 72 GLU cc_start: 0.5928 (pp20) cc_final: 0.5002 (pp20) REVERT: e 82 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7306 (mm-40) REVERT: e 93 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6643 (mp0) outliers start: 113 outliers final: 88 residues processed: 580 average time/residue: 0.4964 time to fit residues: 465.8828 Evaluate side-chains 569 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 475 time to evaluate : 4.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 518 ASP Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 164 HIS Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 268 ASN Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 419 ASP Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 523 ASN Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 237 ASN Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 433 GLN Chi-restraints excluded: chain Q residue 445 THR Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain O residue 501 SER Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 237 ASN Chi-restraints excluded: chain P residue 439 VAL Chi-restraints excluded: chain P residue 455 LEU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 225 LEU Chi-restraints excluded: chain g residue 104 CYS Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 82 GLN Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 403 optimal weight: 9.9990 chunk 424 optimal weight: 2.9990 chunk 387 optimal weight: 0.6980 chunk 413 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 324 optimal weight: 0.0970 chunk 126 optimal weight: 9.9990 chunk 373 optimal weight: 3.9990 chunk 390 optimal weight: 10.0000 chunk 411 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN ** U 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 ASN ** N 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36854 Z= 0.201 Angle : 0.550 12.579 49840 Z= 0.282 Chirality : 0.044 0.263 5616 Planarity : 0.004 0.061 6505 Dihedral : 5.077 75.576 5094 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.97 % Allowed : 21.93 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -1.81 (0.12), residues: 4623 helix: -0.62 (0.12), residues: 1967 sheet: -1.18 (0.21), residues: 596 loop : -1.71 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP N 450 HIS 0.006 0.001 HIS U 97 PHE 0.019 0.001 PHE d 141 TYR 0.023 0.001 TYR P 423 ARG 0.007 0.000 ARG L 571 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 476 time to evaluate : 3.736 Fit side-chains REVERT: L 151 ASP cc_start: 0.7451 (m-30) cc_final: 0.7076 (m-30) REVERT: L 200 LYS cc_start: 0.5989 (ttmt) cc_final: 0.5705 (pttm) REVERT: L 235 ASP cc_start: 0.7971 (m-30) cc_final: 0.7741 (m-30) REVERT: L 484 GLN cc_start: 0.6229 (tp-100) cc_final: 0.5662 (tp40) REVERT: L 485 GLU cc_start: 0.6817 (tt0) cc_final: 0.5237 (mm-30) REVERT: L 556 GLU cc_start: 0.5378 (OUTLIER) cc_final: 0.4106 (tm-30) REVERT: L 596 LYS cc_start: 0.6572 (mtmm) cc_final: 0.6079 (tptp) REVERT: D 10 PHE cc_start: 0.6308 (t80) cc_final: 0.5848 (m-80) REVERT: D 119 TYR cc_start: 0.3204 (m-80) cc_final: 0.2968 (m-10) REVERT: U 95 MET cc_start: 0.3908 (mmp) cc_final: 0.2268 (ptp) REVERT: U 109 MET cc_start: 0.4505 (mmt) cc_final: 0.3753 (mmm) REVERT: U 111 MET cc_start: 0.4738 (mtt) cc_final: 0.4261 (mmm) REVERT: U 124 ARG cc_start: 0.6043 (ttt180) cc_final: 0.5655 (ttt-90) REVERT: U 173 MET cc_start: 0.2855 (mmm) cc_final: 0.2475 (mmm) REVERT: U 199 TRP cc_start: 0.6137 (t60) cc_final: 0.5351 (t60) REVERT: d 8 VAL cc_start: 0.6154 (OUTLIER) cc_final: 0.5880 (t) REVERT: d 37 GLU cc_start: 0.7254 (tp30) cc_final: 0.6887 (tp30) REVERT: d 68 LYS cc_start: 0.6807 (mttm) cc_final: 0.6557 (tttm) REVERT: d 111 ARG cc_start: 0.6418 (ttp-110) cc_final: 0.6002 (mtp180) REVERT: M 74 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8281 (p) REVERT: M 142 ARG cc_start: 0.6492 (ptp90) cc_final: 0.5765 (mtt180) REVERT: M 234 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7660 (pt) REVERT: M 314 ASN cc_start: 0.7744 (t0) cc_final: 0.7301 (t0) REVERT: M 426 LEU cc_start: 0.8612 (mm) cc_final: 0.8361 (mp) REVERT: M 523 ASN cc_start: 0.8160 (p0) cc_final: 0.7746 (p0) REVERT: N 95 MET cc_start: 0.7834 (mmp) cc_final: 0.7451 (mmp) REVERT: N 163 LYS cc_start: 0.7485 (mmtt) cc_final: 0.7207 (mttp) REVERT: N 550 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5555 (mtt) REVERT: N 597 ILE cc_start: 0.6330 (OUTLIER) cc_final: 0.6076 (mp) REVERT: Q 161 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7588 (tp-100) REVERT: Q 254 MET cc_start: 0.7388 (mmm) cc_final: 0.7067 (mmm) REVERT: Q 360 ASP cc_start: 0.7100 (p0) cc_final: 0.6601 (p0) REVERT: O 88 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7780 (tm-30) REVERT: O 435 MET cc_start: 0.7675 (tpt) cc_final: 0.7396 (tpp) REVERT: P 456 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6527 (mp10) REVERT: b 111 ARG cc_start: 0.7487 (mtp180) cc_final: 0.7162 (mtp-110) REVERT: c 197 GLU cc_start: 0.7849 (mp0) cc_final: 0.7499 (mt-10) REVERT: c 201 ASP cc_start: 0.8049 (m-30) cc_final: 0.7832 (m-30) REVERT: c 219 ASN cc_start: 0.7408 (t0) cc_final: 0.6948 (t0) REVERT: c 225 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6469 (tp) REVERT: g 72 GLU cc_start: 0.5834 (pp20) cc_final: 0.5076 (pp20) REVERT: e 82 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7256 (mm-40) outliers start: 115 outliers final: 95 residues processed: 568 average time/residue: 0.5144 time to fit residues: 476.1917 Evaluate side-chains 565 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 463 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 518 ASP Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 391 ASN Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 162 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 164 HIS Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 288 LEU Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 419 ASP Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 523 ASN Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 597 ILE Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 237 ASN Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 445 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain O residue 501 SER Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 237 ASN Chi-restraints excluded: chain P residue 439 VAL Chi-restraints excluded: chain P residue 455 LEU Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 225 LEU Chi-restraints excluded: chain g residue 104 CYS Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 82 GLN Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 271 optimal weight: 2.9990 chunk 436 optimal weight: 40.0000 chunk 266 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 303 optimal weight: 0.8980 chunk 458 optimal weight: 10.0000 chunk 421 optimal weight: 9.9990 chunk 364 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN ** U 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 ASN N 484 GLN ** N 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36854 Z= 0.187 Angle : 0.544 12.245 49840 Z= 0.279 Chirality : 0.044 0.273 5616 Planarity : 0.004 0.059 6505 Dihedral : 4.963 75.820 5094 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.72 % Allowed : 22.32 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -1.62 (0.12), residues: 4623 helix: -0.44 (0.12), residues: 1966 sheet: -1.06 (0.22), residues: 580 loop : -1.64 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP N 450 HIS 0.006 0.001 HIS U 97 PHE 0.014 0.001 PHE D 199 TYR 0.023 0.001 TYR U 253 ARG 0.008 0.000 ARG L 571 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 480 time to evaluate : 3.910 Fit side-chains REVERT: L 151 ASP cc_start: 0.7463 (m-30) cc_final: 0.7176 (m-30) REVERT: L 200 LYS cc_start: 0.6006 (ttmt) cc_final: 0.5712 (pttm) REVERT: L 235 ASP cc_start: 0.7974 (m-30) cc_final: 0.7745 (m-30) REVERT: L 484 GLN cc_start: 0.6221 (tp-100) cc_final: 0.5660 (tp40) REVERT: L 485 GLU cc_start: 0.6839 (tt0) cc_final: 0.5280 (mm-30) REVERT: L 556 GLU cc_start: 0.5343 (OUTLIER) cc_final: 0.4873 (tp30) REVERT: L 596 LYS cc_start: 0.6525 (mtmm) cc_final: 0.5995 (tptp) REVERT: D 10 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.5742 (m-80) REVERT: D 34 LYS cc_start: 0.7210 (tptm) cc_final: 0.6999 (tptm) REVERT: U 95 MET cc_start: 0.3793 (mmp) cc_final: 0.2327 (ptp) REVERT: U 109 MET cc_start: 0.4517 (mmt) cc_final: 0.3765 (mmm) REVERT: U 111 MET cc_start: 0.4698 (mtt) cc_final: 0.4261 (mmm) REVERT: U 124 ARG cc_start: 0.6065 (ttt180) cc_final: 0.5667 (ttt-90) REVERT: U 173 MET cc_start: 0.2752 (mmm) cc_final: 0.2492 (mmm) REVERT: U 199 TRP cc_start: 0.6119 (t60) cc_final: 0.5361 (t60) REVERT: U 432 GLU cc_start: 0.6492 (mp0) cc_final: 0.5926 (mp0) REVERT: d 8 VAL cc_start: 0.6134 (OUTLIER) cc_final: 0.5864 (t) REVERT: d 37 GLU cc_start: 0.7209 (tp30) cc_final: 0.6876 (tp30) REVERT: d 68 LYS cc_start: 0.6774 (mttm) cc_final: 0.6537 (tttm) REVERT: d 111 ARG cc_start: 0.6397 (ttp-110) cc_final: 0.6001 (mtp180) REVERT: d 184 TYR cc_start: 0.7244 (m-80) cc_final: 0.7018 (m-80) REVERT: M 74 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8321 (p) REVERT: M 142 ARG cc_start: 0.6497 (ptp90) cc_final: 0.5773 (mtt180) REVERT: M 234 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7677 (pt) REVERT: M 314 ASN cc_start: 0.7730 (t0) cc_final: 0.7269 (t0) REVERT: M 426 LEU cc_start: 0.8603 (mm) cc_final: 0.8363 (mp) REVERT: M 523 ASN cc_start: 0.8124 (p0) cc_final: 0.7756 (p0) REVERT: N 95 MET cc_start: 0.7817 (mmp) cc_final: 0.7457 (mmp) REVERT: N 141 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6410 (tp) REVERT: N 163 LYS cc_start: 0.7513 (mmtt) cc_final: 0.7259 (mttp) REVERT: N 550 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5587 (mtt) REVERT: N 597 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.6048 (mp) REVERT: Q 161 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7601 (tp-100) REVERT: Q 360 ASP cc_start: 0.7108 (p0) cc_final: 0.6615 (p0) REVERT: O 88 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7703 (tm-30) REVERT: O 435 MET cc_start: 0.7659 (tpt) cc_final: 0.7412 (tpp) REVERT: P 456 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6521 (mp10) REVERT: b 111 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7189 (mtp-110) REVERT: c 197 GLU cc_start: 0.7838 (mp0) cc_final: 0.7494 (mt-10) REVERT: c 201 ASP cc_start: 0.7991 (m-30) cc_final: 0.7776 (m-30) REVERT: c 219 ASN cc_start: 0.7393 (t0) cc_final: 0.6934 (t0) REVERT: c 225 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6494 (tp) REVERT: g 72 GLU cc_start: 0.5843 (pp20) cc_final: 0.5131 (pp20) REVERT: e 82 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7291 (mm-40) outliers start: 105 outliers final: 90 residues processed: 565 average time/residue: 0.4945 time to fit residues: 450.1058 Evaluate side-chains 570 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 471 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 162 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 164 HIS Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 288 LEU Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain N residue 419 ASP Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 523 ASN Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 597 ILE Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 237 ASN Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 433 GLN Chi-restraints excluded: chain Q residue 445 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain O residue 501 SER Chi-restraints excluded: chain P residue 237 ASN Chi-restraints excluded: chain P residue 439 VAL Chi-restraints excluded: chain P residue 455 LEU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 225 LEU Chi-restraints excluded: chain g residue 104 CYS Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 289 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 336 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 365 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 375 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN ** U 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 ASN ** N 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 421 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 = 0.3612 r_free = 0.3612 target = 0.132607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114475 restraints weight = 59421.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114270 restraints weight = 56179.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114838 restraints weight = 51787.917| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36854 Z= 0.202 Angle : 0.548 12.243 49840 Z= 0.281 Chirality : 0.044 0.262 5616 Planarity : 0.004 0.059 6505 Dihedral : 4.946 76.107 5094 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.97 % Allowed : 22.25 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -1.54 (0.12), residues: 4623 helix: -0.36 (0.12), residues: 1966 sheet: -1.06 (0.22), residues: 584 loop : -1.60 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP N 450 HIS 0.006 0.001 HIS U 97 PHE 0.023 0.001 PHE d 141 TYR 0.042 0.001 TYR U 253 ARG 0.009 0.000 ARG M 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9275.80 seconds wall clock time: 166 minutes 35.93 seconds (9995.93 seconds total)