Starting phenix.real_space_refine on Sun Aug 4 17:33:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/08_2024/6m5r_30090.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/08_2024/6m5r_30090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/08_2024/6m5r_30090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/08_2024/6m5r_30090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/08_2024/6m5r_30090.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/08_2024/6m5r_30090.cif" } resolution = 3.5 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= 0.001 sd= 0.011 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 50 5.16 5 C 7008 2.51 5 N 1996 2.21 5 O 1999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A ASP 302": "OD1" <-> "OD2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B ASP 495": "OD1" <-> "OD2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 523": "NH1" <-> "NH2" Residue "B ARG 531": "NH1" <-> "NH2" Residue "B GLU 537": "OE1" <-> "OE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B GLU 662": "OE1" <-> "OE2" Residue "B TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 687": "NH1" <-> "NH2" Residue "B TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 701": "NH1" <-> "NH2" Residue "B GLU 706": "OE1" <-> "OE2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "B TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 760": "OD1" <-> "OD2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C ASP 31": "OD1" <-> "OD2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ASP 49": "OD1" <-> "OD2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ASP 123": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11055 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 4924 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 30, 'TRANS': 615} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5296 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 35, 'TRANS': 653} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 833 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5857 SG CYS B 121 29.367 53.359 51.647 1.00 29.72 S ATOM 10821 SG CYS C 101 29.841 52.098 54.795 1.00 44.32 S ATOM 6446 SG CYS B 197 52.080 57.130 48.889 1.00 30.65 S ATOM 6464 SG CYS B 200 54.032 56.988 51.829 1.00 34.04 S Time building chain proxies: 6.06, per 1000 atoms: 0.55 Number of scatterers: 11055 At special positions: 0 Unit cell: (109.2, 107.1, 118.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 50 16.00 O 1999 8.00 N 1996 7.00 C 7008 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: 4.25 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B 801 " - pdb=" SG CYS C 101 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 124 " pdb=" ZN B 802 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 197 " pdb="ZN ZN B 802 " - pdb=" ND1 HIS B 225 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 200 " 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 54.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 38 through 42 removed outlier: 4.233A pdb=" N LEU A 41 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 42' Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.481A pdb=" N SER A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.762A pdb=" N LYS A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 119 removed outlier: 4.039A pdb=" N ARG A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Proline residue: A 132 - end of helix removed outlier: 3.863A pdb=" N ASN A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.931A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 3.963A pdb=" N LEU A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 215 " --> pdb=" O HIS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 removed outlier: 4.420A pdb=" N LEU A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.888A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 293 through 308 removed outlier: 3.977A pdb=" N VAL A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N CYS A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 336 through 340 removed outlier: 4.088A pdb=" N SER A 339 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 374 removed outlier: 3.715A pdb=" N ILE A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.545A pdb=" N ASN A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 418 through 424 removed outlier: 4.536A pdb=" N VAL A 421 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A 424 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.554A pdb=" N SER A 458 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 549 through 569 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 639 through 653 Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'B' and resid 6 through 33 removed outlier: 4.024A pdb=" N ARG B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 43 through 58 Processing helix chain 'B' and resid 60 through 70 removed outlier: 4.143A pdb=" N GLY B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.933A pdb=" N THR B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 92 " --> pdb=" O TRP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.606A pdb=" N GLU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 180 removed outlier: 3.919A pdb=" N PHE B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 removed outlier: 4.094A pdb=" N LEU B 204 " --> pdb=" O CYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.604A pdb=" N TYR B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 267 removed outlier: 3.859A pdb=" N LEU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.700A pdb=" N LEU B 311 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN B 312 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 313 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 355 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.987A pdb=" N ILE B 381 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.549A pdb=" N GLN B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.503A pdb=" N VAL B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.616A pdb=" N CYS B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 507 removed outlier: 3.926A pdb=" N ILE B 488 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B 501 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 3.543A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 524 " --> pdb=" O ARG B 520 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 560 removed outlier: 4.056A pdb=" N ALA B 544 " --> pdb=" O PRO B 540 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 587 removed outlier: 4.549A pdb=" N ALA B 578 " --> pdb=" O GLY B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 595 through 608 removed outlier: 3.866A pdb=" N ARG B 602 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 608 " --> pdb=" O PHE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 634 removed outlier: 3.581A pdb=" N SER B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 641 through 646 Processing helix chain 'B' and resid 676 through 700 removed outlier: 3.833A pdb=" N ALA B 681 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 682 " --> pdb=" O THR B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.786A pdb=" N ILE B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.019A pdb=" N ALA C 21 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 61 through 81 removed outlier: 3.533A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 128 removed outlier: 3.640A pdb=" N GLU C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257 Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 removed outlier: 3.940A pdb=" N SER A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 616 through 619 removed outlier: 6.194A pdb=" N VAL A 576 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP A 503 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG A 528 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY A 527 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 535 " --> pdb=" O GLY A 527 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR A 529 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR A 533 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR A 533 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER A 659 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A 535 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU A 661 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA A 537 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 663 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU A 539 " --> pdb=" O VAL A 663 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 707 through 708 removed outlier: 3.691A pdb=" N VAL B 741 " --> pdb=" O VAL B 754 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 754 " --> pdb=" O VAL B 741 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1398 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: 3.27 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2326 1.33 - 1.45: 2610 1.45 - 1.57: 6278 1.57 - 1.69: 3 1.69 - 1.82: 71 Bond restraints: 11288 Sorted by residual: bond pdb=" N ARG A 475 " pdb=" CA ARG A 475 " ideal model delta sigma weight residual 1.455 1.490 -0.036 9.60e-03 1.09e+04 1.39e+01 bond pdb=" CA VAL A 525 " pdb=" CB VAL A 525 " ideal model delta sigma weight residual 1.537 1.581 -0.044 1.26e-02 6.30e+03 1.23e+01 bond pdb=" C ARG A 490 " pdb=" O ARG A 490 " ideal model delta sigma weight residual 1.244 1.211 0.033 1.00e-02 1.00e+04 1.11e+01 bond pdb=" CA LEU A 435 " pdb=" C LEU A 435 " ideal model delta sigma weight residual 1.523 1.567 -0.044 1.34e-02 5.57e+03 1.09e+01 bond pdb=" C GLY A 582 " pdb=" O GLY A 582 " ideal model delta sigma weight residual 1.239 1.216 0.023 7.10e-03 1.98e+04 1.03e+01 ... (remaining 11283 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.67: 254 105.67 - 112.79: 5941 112.79 - 119.91: 3803 119.91 - 127.03: 5216 127.03 - 134.15: 122 Bond angle restraints: 15336 Sorted by residual: angle pdb=" N VAL A 477 " pdb=" CA VAL A 477 " pdb=" C VAL A 477 " ideal model delta sigma weight residual 111.62 115.77 -4.15 7.90e-01 1.60e+00 2.77e+01 angle pdb=" N ARG A 420 " pdb=" CA ARG A 420 " pdb=" C ARG A 420 " ideal model delta sigma weight residual 111.82 106.52 5.30 1.16e+00 7.43e-01 2.08e+01 angle pdb=" O PRO A 624 " pdb=" C PRO A 624 " pdb=" N PRO A 625 " ideal model delta sigma weight residual 121.31 123.27 -1.96 4.60e-01 4.73e+00 1.81e+01 angle pdb=" N VAL A 656 " pdb=" CA VAL A 656 " pdb=" C VAL A 656 " ideal model delta sigma weight residual 108.11 113.87 -5.76 1.40e+00 5.10e-01 1.69e+01 angle pdb=" N PHE A 573 " pdb=" CA PHE A 573 " pdb=" C PHE A 573 " ideal model delta sigma weight residual 109.07 115.58 -6.51 1.61e+00 3.86e-01 1.64e+01 ... (remaining 15331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5991 18.00 - 36.00: 590 36.00 - 53.99: 128 53.99 - 71.99: 21 71.99 - 89.99: 16 Dihedral angle restraints: 6746 sinusoidal: 2576 harmonic: 4170 Sorted by residual: dihedral pdb=" CA CYS B 223 " pdb=" C CYS B 223 " pdb=" N ASN B 224 " pdb=" CA ASN B 224 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" C VAL A 558 " pdb=" N VAL A 558 " pdb=" CA VAL A 558 " pdb=" CB VAL A 558 " ideal model delta harmonic sigma weight residual -122.00 -133.86 11.86 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" N VAL A 558 " pdb=" C VAL A 558 " pdb=" CA VAL A 558 " pdb=" CB VAL A 558 " ideal model delta harmonic sigma weight residual 123.40 134.87 -11.47 0 2.50e+00 1.60e-01 2.11e+01 ... (remaining 6743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1552 0.074 - 0.147: 170 0.147 - 0.221: 27 0.221 - 0.294: 7 0.294 - 0.368: 2 Chirality restraints: 1758 Sorted by residual: chirality pdb=" CA VAL A 558 " pdb=" N VAL A 558 " pdb=" C VAL A 558 " pdb=" CB VAL A 558 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA VAL A 506 " pdb=" N VAL A 506 " pdb=" C VAL A 506 " pdb=" CB VAL A 506 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1755 not shown) Planarity restraints: 2003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 719 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C ALA A 719 " 0.065 2.00e-02 2.50e+03 pdb=" O ALA A 719 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 720 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 720 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C ALA A 720 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 720 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN A 721 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 724 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 725 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 725 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 725 " 0.030 5.00e-02 4.00e+02 ... (remaining 2000 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 112 2.59 - 3.17: 9526 3.17 - 3.75: 16631 3.75 - 4.32: 23010 4.32 - 4.90: 38164 Nonbonded interactions: 87443 Sorted by model distance: nonbonded pdb=" O CYS B 223 " pdb="ZN ZN B 802 " model vdw 2.015 2.230 nonbonded pdb=" OE2 GLU B 30 " pdb=" OG SER B 182 " model vdw 2.208 3.040 nonbonded pdb=" OE1 GLU B 203 " pdb=" NH2 ARG B 221 " model vdw 2.245 3.120 nonbonded pdb=" O GLU B 30 " pdb=" NH1 ARG B 34 " model vdw 2.248 3.120 nonbonded pdb=" CD1 ILE C 17 " pdb=" OE2 GLU C 48 " model vdw 2.256 3.460 ... (remaining 87438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.900 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11288 Z= 0.349 Angle : 0.774 8.576 15336 Z= 0.485 Chirality : 0.052 0.368 1758 Planarity : 0.005 0.055 2003 Dihedral : 15.649 89.991 4042 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.15 % Favored : 90.70 % Rotamer: Outliers : 5.29 % Allowed : 17.28 % Favored : 77.43 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.20), residues: 1420 helix: -1.67 (0.18), residues: 677 sheet: -1.46 (0.49), residues: 106 loop : -3.47 (0.21), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 658 HIS 0.009 0.001 HIS A 540 PHE 0.023 0.002 PHE A 634 TYR 0.018 0.002 TYR A 507 ARG 0.005 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 191 time to evaluate : 1.207 Fit side-chains REVERT: B 38 HIS cc_start: 0.7679 (m90) cc_final: 0.7130 (m-70) REVERT: B 190 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9001 (pp) REVERT: B 375 MET cc_start: 0.8623 (mmm) cc_final: 0.8189 (tpp) REVERT: B 389 ASP cc_start: 0.8496 (t0) cc_final: 0.8232 (t0) REVERT: B 644 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8534 (tt) REVERT: B 665 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7994 (mmt180) REVERT: B 667 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7568 (m-80) outliers start: 60 outliers final: 37 residues processed: 245 average time/residue: 0.2711 time to fit residues: 89.5426 Evaluate side-chains 175 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 102 HIS A 251 GLN A 343 ASN A 351 ASN A 359 ASN A 367 GLN A 670 GLN B 46 GLN B 53 GLN B 124 HIS B 144 HIS B 152 GLN B 323 GLN B 522 GLN B 579 HIS B 614 HIS B 621 GLN C 103 HIS C 126 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11288 Z= 0.260 Angle : 0.646 8.490 15336 Z= 0.329 Chirality : 0.043 0.286 1758 Planarity : 0.004 0.050 2003 Dihedral : 7.449 59.131 1643 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.21 % Favored : 89.72 % Rotamer: Outliers : 5.82 % Allowed : 19.22 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.52 (0.22), residues: 1420 helix: -0.65 (0.20), residues: 685 sheet: -1.35 (0.49), residues: 106 loop : -2.95 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 658 HIS 0.007 0.001 HIS A 646 PHE 0.019 0.002 PHE A 633 TYR 0.017 0.001 TYR A 397 ARG 0.004 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 149 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 405 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7410 (pt0) REVERT: A 509 ASP cc_start: 0.5621 (t0) cc_final: 0.5171 (t0) REVERT: A 707 ASP cc_start: 0.5100 (p0) cc_final: 0.4868 (p0) REVERT: B 38 HIS cc_start: 0.7733 (m90) cc_final: 0.7125 (m-70) REVERT: B 389 ASP cc_start: 0.8465 (t0) cc_final: 0.8214 (t0) REVERT: B 644 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8549 (tt) REVERT: B 667 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7466 (m-80) outliers start: 66 outliers final: 40 residues processed: 208 average time/residue: 0.2410 time to fit residues: 71.1845 Evaluate side-chains 174 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 0.0570 chunk 115 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN A 102 HIS A 155 GLN A 211 HIS A 340 HIS A 367 GLN B 195 HIS ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11288 Z= 0.169 Angle : 0.605 8.705 15336 Z= 0.303 Chirality : 0.041 0.222 1758 Planarity : 0.004 0.041 2003 Dihedral : 6.300 59.544 1609 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.37 % Favored : 90.56 % Rotamer: Outliers : 5.47 % Allowed : 19.22 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.22), residues: 1420 helix: -0.11 (0.20), residues: 690 sheet: -1.24 (0.49), residues: 103 loop : -2.79 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 658 HIS 0.006 0.001 HIS B 535 PHE 0.021 0.001 PHE A 360 TYR 0.020 0.001 TYR A 533 ARG 0.005 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 161 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7823 (mm) REVERT: A 405 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7344 (pt0) REVERT: A 443 MET cc_start: 0.7786 (mpp) cc_final: 0.4523 (ptt) REVERT: A 509 ASP cc_start: 0.6182 (t0) cc_final: 0.5942 (t0) REVERT: B 38 HIS cc_start: 0.7758 (m90) cc_final: 0.6940 (m90) REVERT: B 370 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8134 (mm) REVERT: B 389 ASP cc_start: 0.8385 (t0) cc_final: 0.8164 (t0) REVERT: B 411 ARG cc_start: 0.7482 (ptm160) cc_final: 0.7243 (ptm160) REVERT: B 605 GLU cc_start: 0.7692 (tt0) cc_final: 0.7402 (tt0) REVERT: B 629 TYR cc_start: 0.9056 (m-10) cc_final: 0.8427 (m-80) REVERT: B 644 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8547 (tt) REVERT: B 667 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7217 (m-80) outliers start: 62 outliers final: 40 residues processed: 211 average time/residue: 0.2264 time to fit residues: 68.1271 Evaluate side-chains 179 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 601 HIS Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 86 optimal weight: 0.0040 chunk 129 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 86 ASN A 367 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11288 Z= 0.241 Angle : 0.614 8.122 15336 Z= 0.308 Chirality : 0.042 0.221 1758 Planarity : 0.004 0.038 2003 Dihedral : 6.149 59.687 1607 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.37 % Favored : 90.56 % Rotamer: Outliers : 5.64 % Allowed : 20.81 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.23), residues: 1420 helix: 0.08 (0.20), residues: 699 sheet: -1.19 (0.53), residues: 88 loop : -2.55 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 658 HIS 0.005 0.001 HIS B 535 PHE 0.018 0.001 PHE A 573 TYR 0.015 0.001 TYR A 533 ARG 0.005 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 144 time to evaluate : 1.218 Fit side-chains REVERT: A 274 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7957 (mm) REVERT: A 316 HIS cc_start: 0.5599 (t-170) cc_final: 0.5287 (t-170) REVERT: A 405 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7369 (pt0) REVERT: B 38 HIS cc_start: 0.7926 (m90) cc_final: 0.7128 (m90) REVERT: B 370 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8230 (mm) REVERT: B 389 ASP cc_start: 0.8466 (t0) cc_final: 0.8155 (t0) REVERT: B 644 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8566 (tt) REVERT: B 667 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.7348 (m-80) outliers start: 64 outliers final: 44 residues processed: 197 average time/residue: 0.2350 time to fit residues: 66.0906 Evaluate side-chains 179 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 131 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 155 GLN A 367 GLN B 770 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11288 Z= 0.304 Angle : 0.649 10.766 15336 Z= 0.323 Chirality : 0.043 0.187 1758 Planarity : 0.004 0.039 2003 Dihedral : 6.150 58.611 1604 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.21 % Favored : 89.72 % Rotamer: Outliers : 6.61 % Allowed : 20.28 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.23), residues: 1420 helix: 0.12 (0.20), residues: 699 sheet: -1.00 (0.52), residues: 93 loop : -2.51 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 658 HIS 0.004 0.001 HIS B 535 PHE 0.017 0.002 PHE A 633 TYR 0.012 0.001 TYR A 533 ARG 0.006 0.000 ARG B 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 139 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8110 (mm) REVERT: A 306 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7652 (ttm110) REVERT: A 405 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7422 (pt0) REVERT: A 443 MET cc_start: 0.7607 (mpp) cc_final: 0.4371 (ptt) REVERT: B 38 HIS cc_start: 0.7937 (m90) cc_final: 0.7668 (m90) REVERT: B 370 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8214 (mm) REVERT: B 389 ASP cc_start: 0.8474 (t0) cc_final: 0.8138 (t0) REVERT: B 644 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8607 (tt) outliers start: 75 outliers final: 56 residues processed: 201 average time/residue: 0.2391 time to fit residues: 68.8252 Evaluate side-chains 185 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 126 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 137 optimal weight: 0.9990 chunk 114 optimal weight: 0.0370 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 45 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11288 Z= 0.151 Angle : 0.592 8.678 15336 Z= 0.294 Chirality : 0.041 0.210 1758 Planarity : 0.004 0.036 2003 Dihedral : 5.860 58.133 1604 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 4.59 % Allowed : 22.40 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1420 helix: 0.40 (0.21), residues: 704 sheet: -0.97 (0.54), residues: 93 loop : -2.36 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 658 HIS 0.004 0.001 HIS A 646 PHE 0.016 0.001 PHE A 241 TYR 0.014 0.001 TYR A 397 ARG 0.007 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 148 time to evaluate : 1.283 Fit side-chains REVERT: A 166 LEU cc_start: 0.8627 (tt) cc_final: 0.8335 (tt) REVERT: A 336 PHE cc_start: 0.6589 (m-80) cc_final: 0.6253 (m-80) REVERT: A 405 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7270 (pt0) REVERT: A 443 MET cc_start: 0.7599 (mpp) cc_final: 0.4204 (ptt) REVERT: B 370 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8140 (mm) REVERT: B 375 MET cc_start: 0.8277 (tpp) cc_final: 0.7455 (tpp) REVERT: B 389 ASP cc_start: 0.8436 (t0) cc_final: 0.8117 (t0) REVERT: B 629 TYR cc_start: 0.9031 (m-10) cc_final: 0.8395 (m-80) REVERT: B 644 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8510 (tt) outliers start: 52 outliers final: 40 residues processed: 190 average time/residue: 0.2177 time to fit residues: 59.7646 Evaluate side-chains 166 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 77 optimal weight: 0.0870 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 136 optimal weight: 0.0270 chunk 85 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS C 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11288 Z= 0.151 Angle : 0.584 8.305 15336 Z= 0.289 Chirality : 0.040 0.193 1758 Planarity : 0.003 0.036 2003 Dihedral : 5.484 58.187 1600 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 4.32 % Allowed : 22.75 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1420 helix: 0.69 (0.21), residues: 697 sheet: -0.97 (0.54), residues: 93 loop : -2.26 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 308 HIS 0.006 0.001 HIS B 38 PHE 0.019 0.001 PHE A 573 TYR 0.007 0.001 TYR A 533 ARG 0.007 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 1.218 Fit side-chains REVERT: A 443 MET cc_start: 0.7595 (mpp) cc_final: 0.4258 (ptt) REVERT: A 714 MET cc_start: 0.7671 (mpp) cc_final: 0.7421 (mpp) REVERT: B 389 ASP cc_start: 0.8390 (t0) cc_final: 0.8064 (t0) REVERT: B 629 TYR cc_start: 0.8977 (m-10) cc_final: 0.8522 (m-10) REVERT: B 644 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8575 (tt) outliers start: 49 outliers final: 37 residues processed: 180 average time/residue: 0.2321 time to fit residues: 59.3488 Evaluate side-chains 160 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 601 HIS Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11288 Z= 0.241 Angle : 0.616 8.543 15336 Z= 0.303 Chirality : 0.042 0.186 1758 Planarity : 0.004 0.037 2003 Dihedral : 5.595 58.063 1600 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 4.59 % Allowed : 23.10 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1420 helix: 0.63 (0.21), residues: 702 sheet: -1.25 (0.51), residues: 106 loop : -2.26 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 308 HIS 0.004 0.001 HIS C 125 PHE 0.018 0.002 PHE A 241 TYR 0.008 0.001 TYR C 68 ARG 0.007 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 128 time to evaluate : 0.998 Fit side-chains REVERT: A 443 MET cc_start: 0.7604 (mpp) cc_final: 0.4280 (ptt) REVERT: B 389 ASP cc_start: 0.8486 (t0) cc_final: 0.8158 (t0) REVERT: B 629 TYR cc_start: 0.9037 (m-10) cc_final: 0.8443 (m-80) REVERT: B 644 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8625 (tt) outliers start: 52 outliers final: 45 residues processed: 173 average time/residue: 0.2353 time to fit residues: 57.7502 Evaluate side-chains 162 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 116 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.0470 chunk 127 optimal weight: 0.0470 chunk 131 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 621 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11288 Z= 0.160 Angle : 0.603 8.871 15336 Z= 0.298 Chirality : 0.041 0.202 1758 Planarity : 0.004 0.045 2003 Dihedral : 5.500 58.598 1600 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 3.70 % Allowed : 24.16 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1420 helix: 0.75 (0.21), residues: 702 sheet: -1.22 (0.52), residues: 98 loop : -2.20 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 658 HIS 0.004 0.001 HIS A 646 PHE 0.014 0.001 PHE A 241 TYR 0.008 0.001 TYR A 533 ARG 0.010 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 128 time to evaluate : 1.269 Fit side-chains REVERT: A 336 PHE cc_start: 0.6334 (m-80) cc_final: 0.5852 (m-80) REVERT: A 443 MET cc_start: 0.7590 (mpp) cc_final: 0.4252 (ptt) REVERT: B 375 MET cc_start: 0.8280 (tpp) cc_final: 0.7554 (tpp) REVERT: B 389 ASP cc_start: 0.8419 (t0) cc_final: 0.8091 (t0) REVERT: B 629 TYR cc_start: 0.8982 (m-10) cc_final: 0.8486 (m-10) REVERT: B 644 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8591 (tt) outliers start: 42 outliers final: 39 residues processed: 165 average time/residue: 0.2357 time to fit residues: 57.2403 Evaluate side-chains 163 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.8596 > 50: distance: 93 - 98: 9.372 distance: 98 - 99: 26.202 distance: 99 - 100: 18.112 distance: 100 - 101: 17.411 distance: 100 - 102: 25.600 distance: 102 - 103: 19.165 distance: 103 - 104: 17.079 distance: 103 - 106: 22.623 distance: 104 - 105: 17.414 distance: 104 - 108: 5.718 distance: 106 - 107: 13.135 distance: 108 - 109: 45.210 distance: 109 - 110: 35.859 distance: 110 - 111: 9.610 distance: 110 - 112: 31.987 distance: 112 - 113: 16.247 distance: 113 - 114: 14.700 distance: 113 - 116: 11.192 distance: 114 - 115: 27.950 distance: 114 - 120: 26.689 distance: 116 - 117: 12.421 distance: 117 - 118: 3.619 distance: 117 - 119: 6.543 distance: 120 - 121: 13.511 distance: 121 - 122: 20.969 distance: 121 - 124: 25.511 distance: 122 - 123: 11.490 distance: 122 - 128: 12.775 distance: 124 - 125: 13.005 distance: 124 - 126: 11.380 distance: 125 - 127: 3.636 distance: 128 - 129: 22.899 distance: 129 - 130: 52.434 distance: 129 - 132: 23.069 distance: 130 - 131: 43.281 distance: 130 - 135: 51.764 distance: 132 - 133: 8.324 distance: 132 - 134: 14.189 distance: 135 - 136: 53.860 distance: 135 - 141: 34.001 distance: 136 - 137: 31.837 distance: 136 - 139: 28.541 distance: 137 - 138: 26.703 distance: 137 - 142: 27.092 distance: 139 - 140: 11.094 distance: 140 - 141: 19.609 distance: 142 - 143: 23.890 distance: 142 - 148: 30.971 distance: 143 - 144: 34.372 distance: 143 - 146: 39.672 distance: 144 - 145: 32.378 distance: 144 - 149: 30.343 distance: 146 - 147: 11.385 distance: 147 - 148: 25.469 distance: 149 - 150: 13.867 distance: 150 - 151: 20.680 distance: 150 - 153: 16.550 distance: 151 - 152: 15.472 distance: 151 - 154: 6.621 distance: 154 - 155: 34.389 distance: 155 - 156: 48.193 distance: 155 - 158: 12.079 distance: 156 - 157: 37.037 distance: 156 - 162: 24.673 distance: 158 - 159: 6.970 distance: 159 - 160: 18.179 distance: 159 - 161: 27.277