Starting phenix.real_space_refine on Wed Feb 14 08:01:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjm_33874/02_2024/7yjm_33874_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjm_33874/02_2024/7yjm_33874.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjm_33874/02_2024/7yjm_33874_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjm_33874/02_2024/7yjm_33874_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjm_33874/02_2024/7yjm_33874_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjm_33874/02_2024/7yjm_33874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjm_33874/02_2024/7yjm_33874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjm_33874/02_2024/7yjm_33874_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjm_33874/02_2024/7yjm_33874_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 P 1 5.49 5 S 50 5.16 5 C 5742 2.51 5 N 1500 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 66": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ASP 93": "OD1" <-> "OD2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "C ARG 6": "NH1" <-> "NH2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 45": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8895 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3230 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "B" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3673 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 21, 'TRANS': 449} Chain breaks: 1 Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1277 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 218 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 436 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.58 Number of scatterers: 8895 At special positions: 0 Unit cell: (88.56, 81, 118.8, 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) S 50 16.00 P 1 15.00 O 1602 8.00 N 1500 7.00 C 5742 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.9 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 5 sheets defined 34.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.789A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 72' Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.548A pdb=" N GLU A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 183 through 186 No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.581A pdb=" N GLY A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.575A pdb=" N ILE A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 270 No H-bonds generated for 'chain 'A' and resid 267 through 270' Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.556A pdb=" N ALA A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 377 removed outlier: 4.035A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 425 removed outlier: 3.633A pdb=" N LEU A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 430 No H-bonds generated for 'chain 'A' and resid 427 through 430' Processing helix chain 'A' and resid 469 through 476 removed outlier: 3.747A pdb=" N LEU A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 8 No H-bonds generated for 'chain 'B' and resid 6 through 8' Processing helix chain 'B' and resid 13 through 16 No H-bonds generated for 'chain 'B' and resid 13 through 16' Processing helix chain 'B' and resid 18 through 21 No H-bonds generated for 'chain 'B' and resid 18 through 21' Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 146 through 149 No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 151 through 159 removed outlier: 3.649A pdb=" N VAL B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 217 through 230 removed outlier: 3.987A pdb=" N ARG B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.532A pdb=" N ALA B 264 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 294 No H-bonds generated for 'chain 'B' and resid 291 through 294' Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.581A pdb=" N HIS B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.716A pdb=" N GLN B 350 " --> pdb=" O PRO B 346 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 388 removed outlier: 3.965A pdb=" N LYS B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 419 Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.717A pdb=" N LYS B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 44 removed outlier: 3.527A pdb=" N LEU D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 44 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.559A pdb=" N HIS D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 61 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'D' and resid 88 through 95 removed outlier: 5.908A pdb=" N ASP D 93 " --> pdb=" O TRP D 89 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 4.188A pdb=" N VAL D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'E' and resid 38 through 53 removed outlier: 3.824A pdb=" N GLY E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 51 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.652A pdb=" N TYR C 9 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 29 removed outlier: 3.579A pdb=" N TYR C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.767A pdb=" N ASN C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.595A pdb=" N VAL A 111 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 171 through 175 removed outlier: 3.625A pdb=" N GLY A 327 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE A 279 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 249 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ASP A 281 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA A 251 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 195 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL A 250 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 197 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLU A 252 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR A 216 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 390 through 392 removed outlier: 3.729A pdb=" N ILE A 451 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.552A pdb=" N GLY B 318 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 319 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 304 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR B 308 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B 208 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N SER B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG B 210 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 426 through 428 removed outlier: 3.781A pdb=" N VAL B 426 " --> pdb=" O ARG B 441 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 525 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: 2.26 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2778 1.34 - 1.45: 1359 1.45 - 1.57: 4888 1.57 - 1.69: 1 1.69 - 1.81: 78 Bond restraints: 9104 Sorted by residual: bond pdb=" C14 Z1T D 201 " pdb=" C15 Z1T D 201 " ideal model delta sigma weight residual 1.343 1.522 -0.179 2.00e-02 2.50e+03 8.03e+01 bond pdb=" C19 Z1T D 201 " pdb=" N1 Z1T D 201 " ideal model delta sigma weight residual 1.481 1.333 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C2 PLP B 501 " pdb=" C3 PLP B 501 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C4 PLP B 501 " pdb=" C5 PLP B 501 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C3 PLP B 501 " pdb=" C4 PLP B 501 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.85: 277 106.85 - 113.63: 4989 113.63 - 120.41: 3275 120.41 - 127.19: 3688 127.19 - 133.97: 93 Bond angle restraints: 12322 Sorted by residual: angle pdb=" C14 Z1T D 201 " pdb=" C15 Z1T D 201 " pdb=" C16 Z1T D 201 " ideal model delta sigma weight residual 152.64 114.79 37.85 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C GLY A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta sigma weight residual 119.84 128.25 -8.41 1.25e+00 6.40e-01 4.52e+01 angle pdb=" N LEU A 289 " pdb=" CA LEU A 289 " pdb=" C LEU A 289 " ideal model delta sigma weight residual 111.36 117.75 -6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" N GLU B 230 " pdb=" CA GLU B 230 " pdb=" C GLU B 230 " ideal model delta sigma weight residual 111.28 117.56 -6.28 1.09e+00 8.42e-01 3.32e+01 angle pdb=" C ALA B 133 " pdb=" CA ALA B 133 " pdb=" CB ALA B 133 " ideal model delta sigma weight residual 116.54 110.57 5.97 1.15e+00 7.56e-01 2.69e+01 ... (remaining 12317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4505 17.53 - 35.06: 560 35.06 - 52.59: 265 52.59 - 70.11: 75 70.11 - 87.64: 9 Dihedral angle restraints: 5414 sinusoidal: 2178 harmonic: 3236 Sorted by residual: dihedral pdb=" CG ARG B 455 " pdb=" CD ARG B 455 " pdb=" NE ARG B 455 " pdb=" CZ ARG B 455 " ideal model delta sinusoidal sigma weight residual -90.00 -40.65 -49.35 2 1.50e+01 4.44e-03 1.23e+01 dihedral pdb=" CA ASP B 34 " pdb=" CB ASP B 34 " pdb=" CG ASP B 34 " pdb=" OD1 ASP B 34 " ideal model delta sinusoidal sigma weight residual -30.00 -88.61 58.61 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 430 " pdb=" C ASP A 430 " pdb=" N SER A 431 " pdb=" CA SER A 431 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1126 0.073 - 0.147: 210 0.147 - 0.220: 24 0.220 - 0.293: 12 0.293 - 0.367: 2 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA TYR D 122 " pdb=" N TYR D 122 " pdb=" C TYR D 122 " pdb=" CB TYR D 122 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA ASP D 13 " pdb=" N ASP D 13 " pdb=" C ASP D 13 " pdb=" CB ASP D 13 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA LYS B 311 " pdb=" N LYS B 311 " pdb=" C LYS B 311 " pdb=" CB LYS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1371 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 225 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C MET A 225 " -0.038 2.00e-02 2.50e+03 pdb=" O MET A 225 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 226 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 58 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO E 59 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 59 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 59 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 169 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 170 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.026 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 42 2.54 - 3.13: 6370 3.13 - 3.72: 12545 3.72 - 4.31: 18351 4.31 - 4.90: 31849 Nonbonded interactions: 69157 Sorted by model distance: nonbonded pdb=" OE1 GLU A 321 " pdb=" N GLY A 322 " model vdw 1.946 2.520 nonbonded pdb=" O SER A 98 " pdb=" OG SER A 98 " model vdw 2.208 2.440 nonbonded pdb=" O PHE B 430 " pdb=" O THR B 433 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASN B 215 " pdb=" ND1 HIS B 258 " model vdw 2.292 2.520 nonbonded pdb=" OD2 ASP B 117 " pdb=" NH2 ARG B 366 " model vdw 2.295 2.520 ... (remaining 69152 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 4.130 Check model and map are aligned: 0.180 Set scattering table: 0.090 Process input model: 27.330 Find NCS groups from input model: 0.260 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.179 9104 Z= 0.440 Angle : 1.077 37.848 12322 Z= 0.712 Chirality : 0.061 0.367 1374 Planarity : 0.005 0.047 1544 Dihedral : 19.607 87.642 3340 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.39 % Favored : 89.44 % Rotamer: Outliers : 17.31 % Allowed : 9.64 % Favored : 73.06 % 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: -4.69 (0.21), residues: 1108 helix: -3.60 (0.17), residues: 505 sheet: -1.38 (0.49), residues: 113 loop : -2.87 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 239 HIS 0.007 0.001 HIS B 214 PHE 0.020 0.001 PHE A 220 TYR 0.014 0.001 TYR B 406 ARG 0.002 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 99 time to evaluate : 1.084 Fit side-chains REVERT: A 87 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: A 91 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7440 (p-80) REVERT: A 147 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.9017 (mmm160) REVERT: A 153 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8690 (mm) REVERT: A 192 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8522 (tttp) REVERT: A 246 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7472 (mtm180) REVERT: A 291 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7265 (ptm-80) REVERT: A 390 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8378 (mtp) REVERT: A 411 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7334 (p) REVERT: A 439 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7237 (mtt-85) REVERT: B 1 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.5220 (tpp) REVERT: B 31 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6621 (mtm-85) REVERT: B 47 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6883 (pt) REVERT: B 64 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: B 90 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7384 (m110) REVERT: B 118 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7604 (pp20) REVERT: B 130 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8467 (tttm) REVERT: B 437 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8522 (mp) REVERT: D 29 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9078 (m) REVERT: D 72 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8776 (mtmm) REVERT: D 84 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8498 (m110) REVERT: D 100 ARG cc_start: 0.8358 (ttt-90) cc_final: 0.8073 (ttt-90) REVERT: C 27 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8414 (tt) REVERT: C 35 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9332 (tp) REVERT: C 46 TYR cc_start: 0.5378 (OUTLIER) cc_final: 0.4344 (t80) outliers start: 167 outliers final: 100 residues processed: 238 average time/residue: 0.2900 time to fit residues: 88.0080 Evaluate side-chains 216 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 92 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 46 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 28 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 459 HIS B 214 HIS ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9104 Z= 0.147 Angle : 0.556 8.904 12322 Z= 0.290 Chirality : 0.042 0.170 1374 Planarity : 0.005 0.051 1544 Dihedral : 13.184 89.712 1554 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.42 % Favored : 95.22 % Rotamer: Outliers : 4.97 % Allowed : 17.72 % Favored : 77.31 % 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: -3.69 (0.23), residues: 1108 helix: -2.85 (0.20), residues: 503 sheet: -1.08 (0.50), residues: 119 loop : -2.19 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 239 HIS 0.005 0.001 HIS B 214 PHE 0.013 0.001 PHE B 212 TYR 0.017 0.001 TYR B 171 ARG 0.006 0.001 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 107 time to evaluate : 1.183 Fit side-chains REVERT: A 87 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7526 (pt0) REVERT: A 182 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8143 (mmm) REVERT: A 414 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7582 (t0) REVERT: A 420 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: B 47 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7232 (pt) REVERT: B 375 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7046 (ttt-90) REVERT: D 118 HIS cc_start: 0.7689 (t70) cc_final: 0.7156 (t-90) outliers start: 48 outliers final: 28 residues processed: 146 average time/residue: 0.2523 time to fit residues: 48.8482 Evaluate side-chains 130 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9104 Z= 0.343 Angle : 0.598 9.284 12322 Z= 0.311 Chirality : 0.046 0.146 1374 Planarity : 0.005 0.055 1544 Dihedral : 10.472 81.855 1327 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 5.08 % Allowed : 18.24 % Favored : 76.68 % 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: -3.27 (0.24), residues: 1108 helix: -2.43 (0.20), residues: 509 sheet: -0.83 (0.52), residues: 122 loop : -2.08 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 239 HIS 0.005 0.001 HIS A 203 PHE 0.020 0.002 PHE A 220 TYR 0.018 0.002 TYR B 85 ARG 0.005 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 94 time to evaluate : 1.091 Fit side-chains REVERT: A 86 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8971 (m) REVERT: A 153 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8506 (mm) REVERT: A 294 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.7916 (mmt90) REVERT: A 379 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9110 (tt) REVERT: A 414 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7574 (t0) REVERT: A 420 GLU cc_start: 0.8033 (tp30) cc_final: 0.7789 (tt0) REVERT: B 18 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8753 (mp) REVERT: B 98 LYS cc_start: 0.8035 (tttp) cc_final: 0.7203 (tptp) REVERT: B 177 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 374 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8984 (tp) REVERT: B 375 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7234 (ttt-90) REVERT: C 27 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8489 (tt) outliers start: 49 outliers final: 34 residues processed: 134 average time/residue: 0.2427 time to fit residues: 43.9208 Evaluate side-chains 137 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 93 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.8528 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9104 Z= 0.189 Angle : 0.508 8.269 12322 Z= 0.264 Chirality : 0.043 0.135 1374 Planarity : 0.004 0.055 1544 Dihedral : 9.623 81.755 1313 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.15 % Favored : 95.58 % Rotamer: Outliers : 4.66 % Allowed : 19.59 % Favored : 75.75 % 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: -2.71 (0.24), residues: 1108 helix: -1.90 (0.22), residues: 499 sheet: -0.53 (0.53), residues: 122 loop : -1.90 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 239 HIS 0.003 0.001 HIS A 203 PHE 0.016 0.001 PHE A 220 TYR 0.014 0.001 TYR B 171 ARG 0.004 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 98 time to evaluate : 0.985 Fit side-chains REVERT: A 86 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8948 (m) REVERT: A 153 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8415 (mm) REVERT: A 182 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8147 (mmm) REVERT: A 294 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.7917 (mmt90) REVERT: A 414 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7734 (t0) REVERT: A 420 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: B 18 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8692 (mp) REVERT: B 98 LYS cc_start: 0.7929 (tttp) cc_final: 0.7169 (tptp) REVERT: B 375 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7181 (ttt-90) REVERT: C 27 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8501 (tt) outliers start: 45 outliers final: 28 residues processed: 133 average time/residue: 0.2524 time to fit residues: 45.0784 Evaluate side-chains 130 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 93 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 0.0570 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9104 Z= 0.285 Angle : 0.552 7.626 12322 Z= 0.288 Chirality : 0.045 0.178 1374 Planarity : 0.004 0.055 1544 Dihedral : 9.238 82.351 1302 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.78 % Favored : 93.95 % Rotamer: Outliers : 5.18 % Allowed : 20.10 % Favored : 74.72 % 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: -2.48 (0.25), residues: 1108 helix: -1.68 (0.22), residues: 502 sheet: -0.31 (0.53), residues: 120 loop : -1.82 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 239 HIS 0.004 0.001 HIS A 203 PHE 0.019 0.001 PHE A 220 TYR 0.016 0.002 TYR B 85 ARG 0.003 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 94 time to evaluate : 1.056 Fit side-chains REVERT: A 86 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8963 (m) REVERT: A 153 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8457 (mm) REVERT: A 294 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.7935 (mmt90) REVERT: A 414 ASP cc_start: 0.7993 (m-30) cc_final: 0.7777 (t0) REVERT: A 420 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: A 430 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8197 (p0) REVERT: B 18 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8759 (mp) REVERT: B 98 LYS cc_start: 0.8043 (tttp) cc_final: 0.7253 (tptp) REVERT: B 177 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8700 (mp) REVERT: B 375 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7696 (ttt-90) REVERT: C 27 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8487 (tt) outliers start: 50 outliers final: 34 residues processed: 136 average time/residue: 0.2458 time to fit residues: 44.5961 Evaluate side-chains 135 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 92 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9104 Z= 0.217 Angle : 0.512 6.912 12322 Z= 0.266 Chirality : 0.043 0.136 1374 Planarity : 0.004 0.054 1544 Dihedral : 8.903 81.902 1298 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.69 % Favored : 95.04 % Rotamer: Outliers : 4.35 % Allowed : 21.14 % Favored : 74.51 % 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: -2.20 (0.25), residues: 1108 helix: -1.40 (0.23), residues: 503 sheet: -0.20 (0.53), residues: 120 loop : -1.74 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 239 HIS 0.003 0.001 HIS A 203 PHE 0.017 0.001 PHE A 220 TYR 0.014 0.001 TYR B 85 ARG 0.003 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 92 time to evaluate : 1.076 Fit side-chains REVERT: A 86 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8938 (m) REVERT: A 153 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8434 (mm) REVERT: A 294 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.7912 (mmt90) REVERT: A 414 ASP cc_start: 0.7972 (m-30) cc_final: 0.7772 (t0) REVERT: A 420 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: A 430 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8161 (p0) REVERT: B 18 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8725 (mp) REVERT: B 98 LYS cc_start: 0.7965 (tttp) cc_final: 0.7221 (tptp) REVERT: B 177 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8639 (mp) REVERT: C 27 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8460 (tt) outliers start: 42 outliers final: 31 residues processed: 129 average time/residue: 0.2517 time to fit residues: 43.3904 Evaluate side-chains 131 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 92 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8503 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9104 Z= 0.143 Angle : 0.471 6.339 12322 Z= 0.245 Chirality : 0.042 0.137 1374 Planarity : 0.004 0.053 1544 Dihedral : 8.200 79.996 1290 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.51 % Favored : 95.22 % Rotamer: Outliers : 3.94 % Allowed : 21.35 % Favored : 74.72 % 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: -1.80 (0.25), residues: 1108 helix: -0.98 (0.24), residues: 502 sheet: -0.18 (0.50), residues: 132 loop : -1.62 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 23 HIS 0.002 0.000 HIS A 203 PHE 0.012 0.001 PHE A 220 TYR 0.019 0.001 TYR C 41 ARG 0.003 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 90 time to evaluate : 1.001 Fit side-chains REVERT: A 86 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8903 (m) REVERT: A 153 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 182 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8086 (mmm) REVERT: A 294 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7822 (mmt90) REVERT: A 430 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8119 (p0) REVERT: B 98 LYS cc_start: 0.7863 (tttp) cc_final: 0.7097 (tptp) REVERT: B 177 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8555 (mp) REVERT: C 27 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8465 (tt) outliers start: 38 outliers final: 26 residues processed: 122 average time/residue: 0.2431 time to fit residues: 39.6206 Evaluate side-chains 121 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8499 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9104 Z= 0.146 Angle : 0.476 6.168 12322 Z= 0.248 Chirality : 0.042 0.138 1374 Planarity : 0.004 0.053 1544 Dihedral : 8.013 78.984 1289 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.42 % Favored : 95.31 % Rotamer: Outliers : 3.73 % Allowed : 21.45 % Favored : 74.82 % 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: -1.52 (0.26), residues: 1108 helix: -0.69 (0.24), residues: 505 sheet: -0.12 (0.50), residues: 132 loop : -1.52 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 23 HIS 0.002 0.000 HIS A 203 PHE 0.012 0.001 PHE A 220 TYR 0.014 0.001 TYR D 83 ARG 0.002 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 89 time to evaluate : 1.119 Fit side-chains REVERT: A 86 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8882 (m) REVERT: A 153 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8355 (mm) REVERT: A 182 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8079 (mmm) REVERT: A 294 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7742 (mmt90) REVERT: A 430 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8066 (p0) REVERT: B 98 LYS cc_start: 0.7801 (tttp) cc_final: 0.7069 (tptp) REVERT: B 177 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8576 (mp) REVERT: C 27 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8470 (tt) outliers start: 36 outliers final: 27 residues processed: 120 average time/residue: 0.2568 time to fit residues: 41.2936 Evaluate side-chains 122 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 0.0070 chunk 58 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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: 0.8474 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9104 Z= 0.118 Angle : 0.465 7.954 12322 Z= 0.239 Chirality : 0.041 0.138 1374 Planarity : 0.004 0.052 1544 Dihedral : 7.570 77.243 1287 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.06 % Favored : 95.67 % Rotamer: Outliers : 3.32 % Allowed : 21.66 % Favored : 75.03 % 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: -1.22 (0.26), residues: 1108 helix: -0.38 (0.24), residues: 505 sheet: -0.09 (0.50), residues: 132 loop : -1.41 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 23 HIS 0.002 0.000 HIS A 203 PHE 0.011 0.001 PHE B 212 TYR 0.014 0.001 TYR D 83 ARG 0.005 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 93 time to evaluate : 1.255 Fit side-chains REVERT: A 86 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8881 (m) REVERT: A 153 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 294 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7659 (mmt90) REVERT: A 430 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8096 (p0) REVERT: B 65 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8256 (p0) REVERT: B 98 LYS cc_start: 0.7719 (tttp) cc_final: 0.7025 (tptp) REVERT: B 177 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8513 (mp) REVERT: B 306 MET cc_start: 0.8174 (tmm) cc_final: 0.7878 (ttp) REVERT: C 27 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8576 (tt) outliers start: 32 outliers final: 22 residues processed: 121 average time/residue: 0.2848 time to fit residues: 46.4210 Evaluate side-chains 118 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.8507 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9104 Z= 0.188 Angle : 0.498 7.439 12322 Z= 0.257 Chirality : 0.043 0.139 1374 Planarity : 0.004 0.054 1544 Dihedral : 7.622 78.130 1283 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.60 % Favored : 95.13 % Rotamer: Outliers : 3.32 % Allowed : 21.66 % Favored : 75.03 % 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: -1.21 (0.26), residues: 1108 helix: -0.40 (0.24), residues: 516 sheet: -0.02 (0.53), residues: 120 loop : -1.37 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 239 HIS 0.003 0.001 HIS A 203 PHE 0.015 0.001 PHE A 220 TYR 0.014 0.001 TYR B 85 ARG 0.002 0.000 ARG A 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 0.998 Fit side-chains REVERT: A 86 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8908 (m) REVERT: A 153 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 294 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7714 (mmt90) REVERT: A 430 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8026 (p0) REVERT: B 65 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8278 (p0) REVERT: B 98 LYS cc_start: 0.7800 (tttp) cc_final: 0.7074 (tptp) REVERT: B 177 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8639 (mp) REVERT: B 306 MET cc_start: 0.8165 (tmm) cc_final: 0.7827 (ttp) REVERT: C 27 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8517 (tt) outliers start: 32 outliers final: 22 residues processed: 114 average time/residue: 0.2522 time to fit residues: 38.4793 Evaluate side-chains 115 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain C residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 0.0570 chunk 88 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.087811 restraints weight = 12030.986| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.87 r_work: 0.2690 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9104 Z= 0.128 Angle : 0.466 7.271 12322 Z= 0.240 Chirality : 0.042 0.138 1374 Planarity : 0.004 0.052 1544 Dihedral : 7.308 76.711 1281 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.76 % Rotamer: Outliers : 3.21 % Allowed : 21.45 % Favored : 75.34 % 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 (0.26), residues: 1108 helix: -0.02 (0.24), residues: 505 sheet: -0.03 (0.51), residues: 131 loop : -1.31 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 23 HIS 0.002 0.000 HIS A 203 PHE 0.011 0.001 PHE B 212 TYR 0.012 0.001 TYR D 83 ARG 0.002 0.000 ARG A 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2082.72 seconds wall clock time: 38 minutes 30.03 seconds (2310.03 seconds total)