Starting phenix.real_space_refine on Sat Dec 9 12:28:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/12_2023/6m5r_30090.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/12_2023/6m5r_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_30090/12_2023/6m5r_30090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/12_2023/6m5r_30090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/12_2023/6m5r_30090.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5r_30090/12_2023/6m5r_30090.pdb" } 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-1.21rc1-5172/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: 6.34, per 1000 atoms: 0.57 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: 4.30 Conformation dependent library (CDL) restraints added in 2.1 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: 1.08 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: 3.22 Time building geometry restraints manager: 4.63 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 2.440 nonbonded pdb=" OE1 GLU B 203 " pdb=" NH2 ARG B 221 " model vdw 2.245 2.520 nonbonded pdb=" O GLU B 30 " pdb=" NH1 ARG B 34 " model vdw 2.248 2.520 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 ========== 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.930 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.880 Find NCS groups from input model: 0.350 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- 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 : 1.153 Fit side-chains outliers start: 60 outliers final: 37 residues processed: 245 average time/residue: 0.2778 time to fit residues: 91.9161 Evaluate side-chains 173 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1016 time to fit residues: 8.7880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 111 optimal weight: 0.0670 chunk 43 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.1924 ------------------------------------------------------------------------------- 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 135 ASN A 343 ASN A 351 ASN A 359 ASN A 367 GLN A 670 GLN B 38 HIS B 53 GLN B 124 HIS B 152 GLN B 323 GLN ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 HIS B 621 GLN C 103 HIS C 126 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11288 Z= 0.212 Angle : 0.624 9.046 15336 Z= 0.314 Chirality : 0.042 0.287 1758 Planarity : 0.004 0.048 2003 Dihedral : 4.918 26.459 1582 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.86 % Favored : 90.07 % Rotamer: Outliers : 4.41 % Allowed : 19.93 % Favored : 75.66 % 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: -2.47 (0.22), residues: 1420 helix: -0.56 (0.20), residues: 686 sheet: -1.23 (0.50), residues: 103 loop : -3.00 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 658 HIS 0.008 0.001 HIS B 38 PHE 0.019 0.002 PHE A 633 TYR 0.020 0.001 TYR A 397 ARG 0.005 0.000 ARG B 411 *********************** 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 201 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 151 time to evaluate : 1.264 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 194 average time/residue: 0.2387 time to fit residues: 65.2739 Evaluate side-chains 156 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0966 time to fit residues: 6.0660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 155 GLN A 367 GLN B 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11288 Z= 0.176 Angle : 0.596 8.345 15336 Z= 0.296 Chirality : 0.041 0.245 1758 Planarity : 0.004 0.038 2003 Dihedral : 4.683 27.034 1582 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.65 % Favored : 90.28 % Rotamer: Outliers : 2.82 % Allowed : 20.81 % Favored : 76.37 % 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: -1.92 (0.22), residues: 1420 helix: -0.07 (0.20), residues: 691 sheet: -0.99 (0.53), residues: 93 loop : -2.76 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 308 HIS 0.008 0.001 HIS B 535 PHE 0.021 0.001 PHE A 360 TYR 0.019 0.001 TYR A 533 ARG 0.006 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 182 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.270 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 175 average time/residue: 0.2507 time to fit residues: 61.5266 Evaluate side-chains 144 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1002 time to fit residues: 4.6715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 340 HIS A 367 GLN A 408 ASN B 323 GLN B 522 GLN B 770 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2331 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= 0.156 Angle : 0.577 8.742 15336 Z= 0.285 Chirality : 0.040 0.195 1758 Planarity : 0.004 0.037 2003 Dihedral : 4.472 25.970 1582 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.80 % Favored : 91.13 % Rotamer: Outliers : 1.85 % Allowed : 23.19 % Favored : 74.96 % 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: -1.54 (0.23), residues: 1420 helix: 0.25 (0.21), residues: 694 sheet: -0.92 (0.54), residues: 93 loop : -2.56 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 308 HIS 0.008 0.001 HIS A 316 PHE 0.013 0.001 PHE A 298 TYR 0.017 0.001 TYR A 397 ARG 0.004 0.000 ARG B 411 *********************** 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 170 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.227 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 164 average time/residue: 0.2721 time to fit residues: 62.0454 Evaluate side-chains 142 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1061 time to fit residues: 4.3458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 5.9990 chunk 1 optimal weight: 0.0370 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 155 GLN A 341 ASN A 408 ASN B 144 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11288 Z= 0.357 Angle : 0.663 8.074 15336 Z= 0.331 Chirality : 0.044 0.192 1758 Planarity : 0.004 0.039 2003 Dihedral : 4.762 25.686 1582 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.35 % Favored : 89.58 % Rotamer: Outliers : 2.73 % Allowed : 23.54 % Favored : 73.72 % 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: -1.67 (0.23), residues: 1420 helix: 0.06 (0.20), residues: 701 sheet: -0.88 (0.53), residues: 93 loop : -2.58 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 658 HIS 0.005 0.001 HIS A 102 PHE 0.021 0.002 PHE B 72 TYR 0.011 0.001 TYR A 214 ARG 0.005 0.000 ARG B 411 *********************** 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 172 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.218 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 163 average time/residue: 0.2801 time to fit residues: 63.2187 Evaluate side-chains 139 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.262 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1072 time to fit residues: 4.5225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11288 Z= 0.177 Angle : 0.598 11.365 15336 Z= 0.293 Chirality : 0.041 0.164 1758 Planarity : 0.004 0.038 2003 Dihedral : 4.540 25.755 1582 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.15 % Favored : 90.77 % Rotamer: Outliers : 1.68 % Allowed : 24.34 % Favored : 73.99 % 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: -1.39 (0.23), residues: 1420 helix: 0.36 (0.21), residues: 699 sheet: -0.87 (0.54), residues: 93 loop : -2.48 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 658 HIS 0.004 0.001 HIS B 535 PHE 0.020 0.001 PHE A 486 TYR 0.010 0.001 TYR A 533 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 158 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 1.277 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 155 average time/residue: 0.2717 time to fit residues: 58.2419 Evaluate side-chains 130 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1044 time to fit residues: 3.8345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0070 chunk 77 optimal weight: 0.0060 chunk 115 optimal weight: 0.9980 chunk 76 optimal weight: 0.0770 chunk 136 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN B 417 GLN B 770 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11288 Z= 0.149 Angle : 0.582 9.850 15336 Z= 0.286 Chirality : 0.040 0.209 1758 Planarity : 0.003 0.038 2003 Dihedral : 4.323 25.116 1582 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.44 % Favored : 90.49 % Rotamer: Outliers : 1.32 % Allowed : 24.60 % Favored : 74.07 % 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: -1.16 (0.23), residues: 1420 helix: 0.55 (0.21), residues: 700 sheet: -0.86 (0.54), residues: 93 loop : -2.37 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 658 HIS 0.004 0.001 HIS A 646 PHE 0.017 0.001 PHE A 573 TYR 0.008 0.001 TYR A 533 ARG 0.009 0.000 ARG B 60 *********************** 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 150 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.128 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 144 average time/residue: 0.2592 time to fit residues: 52.1248 Evaluate side-chains 127 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1061 time to fit residues: 2.9164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 26 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 67 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 770 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11288 Z= 0.153 Angle : 0.582 9.708 15336 Z= 0.284 Chirality : 0.040 0.198 1758 Planarity : 0.003 0.037 2003 Dihedral : 4.224 25.591 1582 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.01 % Favored : 90.92 % Rotamer: Outliers : 0.88 % Allowed : 24.87 % Favored : 74.25 % 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: -1.00 (0.23), residues: 1420 helix: 0.73 (0.21), residues: 698 sheet: -0.99 (0.53), residues: 96 loop : -2.31 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 308 HIS 0.004 0.001 HIS C 125 PHE 0.016 0.001 PHE A 486 TYR 0.008 0.001 TYR A 286 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 145 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.296 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 142 average time/residue: 0.2712 time to fit residues: 53.5646 Evaluate side-chains 128 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1001 time to fit residues: 2.9713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 0.0010 chunk 131 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 0.0980 chunk 39 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11288 Z= 0.150 Angle : 0.589 9.352 15336 Z= 0.286 Chirality : 0.040 0.198 1758 Planarity : 0.003 0.037 2003 Dihedral : 4.136 24.807 1582 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.15 % Favored : 90.77 % Rotamer: Outliers : 0.62 % Allowed : 25.31 % Favored : 74.07 % 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: -0.89 (0.24), residues: 1420 helix: 0.82 (0.21), residues: 700 sheet: -0.97 (0.54), residues: 96 loop : -2.25 (0.25), residues: 624 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 0.014 0.001 PHE A 486 TYR 0.008 0.001 TYR A 286 ARG 0.007 0.000 ARG A 172 *********************** 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 135 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 1.340 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 133 average time/residue: 0.2572 time to fit residues: 48.7643 Evaluate side-chains 124 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1024 time to fit residues: 2.1399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11288 Z= 0.165 Angle : 0.595 9.877 15336 Z= 0.290 Chirality : 0.041 0.195 1758 Planarity : 0.003 0.037 2003 Dihedral : 4.126 24.961 1582 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.15 % Favored : 90.77 % Rotamer: Outliers : 0.26 % Allowed : 25.57 % Favored : 74.16 % 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: -0.82 (0.24), residues: 1420 helix: 0.88 (0.21), residues: 697 sheet: -0.92 (0.54), residues: 96 loop : -2.20 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 658 HIS 0.004 0.001 HIS C 125 PHE 0.017 0.001 PHE A 298 TYR 0.007 0.001 TYR A 286 ARG 0.007 0.000 ARG A 172 ********************** REFINEMENT MACRO_CYCLE 10 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 129 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.243 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 128 average time/residue: 0.2604 time to fit residues: 47.0358 Evaluate side-chains 121 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1115 time to fit residues: 2.2561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 621 HIS B 210 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.171288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134247 restraints weight = 14842.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134906 restraints weight = 10425.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136137 restraints weight = 9474.293| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11288 Z= 0.336 Angle : 0.670 9.677 15336 Z= 0.329 Chirality : 0.045 0.197 1758 Planarity : 0.004 0.039 2003 Dihedral : 4.497 24.740 1582 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.93 % Favored : 90.00 % Rotamer: Outliers : 0.26 % Allowed : 26.01 % Favored : 73.72 % 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: -1.08 (0.23), residues: 1420 helix: 0.57 (0.21), residues: 697 sheet: -0.68 (0.56), residues: 88 loop : -2.26 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 308 HIS 0.004 0.001 HIS A 102 PHE 0.021 0.002 PHE A 298 TYR 0.011 0.001 TYR A 214 ARG 0.007 0.000 ARG A 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2196.07 seconds wall clock time: 44 minutes 7.59 seconds (2647.59 seconds total)