Starting phenix.real_space_refine on Sat Feb 17 09:56:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/02_2024/8gf6_29979_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/02_2024/8gf6_29979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/02_2024/8gf6_29979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/02_2024/8gf6_29979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/02_2024/8gf6_29979_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/02_2024/8gf6_29979_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 11465 2.51 5 N 3189 2.21 5 O 3550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 353": "OD1" <-> "OD2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 320": "NH1" <-> "NH2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "C ASP 415": "OD1" <-> "OD2" Residue "C PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 146": "OD1" <-> "OD2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 320": "NH1" <-> "NH2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 381": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ASP 398": "OD1" <-> "OD2" Residue "D PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 407": "OE1" <-> "OE2" Residue "D PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 424": "NH1" <-> "NH2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 82": "NH1" <-> "NH2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ASP 114": "OD1" <-> "OD2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F GLU 207": "OE1" <-> "OE2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "X TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18315 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3519 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 18, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MHS:plan-2': 1, 'AGM:plan-2': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3693 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 19, 'TRANS': 464} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MHS:plan-2': 1, 'AGM:plan-2': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3148 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 420} Chain: "D" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3143 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 419} Chain: "E" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "F" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "X" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 9, 'TRANS': 110} Time building chain proxies: 9.81, per 1000 atoms: 0.54 Number of scatterers: 18315 At special positions: 0 Unit cell: (99.235, 102.58, 137.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 3550 8.00 N 3189 7.00 C 11465 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.36 Conformation dependent library (CDL) restraints added in 3.5 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4364 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 111 helices and 11 sheets defined 45.7% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 140 through 152 removed outlier: 3.630A pdb=" N HIS A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 187 No H-bonds generated for 'chain 'A' and resid 184 through 187' Processing helix chain 'A' and resid 198 through 201 No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.717A pdb=" N LYS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 313 through 332 Processing helix chain 'A' and resid 355 through 370 Processing helix chain 'A' and resid 387 through 407 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 418 through 437 Processing helix chain 'A' and resid 440 through 458 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 505 through 518 removed outlier: 3.631A pdb=" N ALA A 512 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 542 through 552 Proline residue: A 545 - end of helix removed outlier: 3.942A pdb=" N PHE A 549 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.925A pdb=" N TRP B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.675A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 153 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 184 through 189 removed outlier: 3.999A pdb=" N GLU B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 198 through 201 No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.556A pdb=" N ALA B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.969A pdb=" N ASP B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'B' and resid 346 through 351 removed outlier: 3.508A pdb=" N ALA B 350 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 370 Processing helix chain 'B' and resid 387 through 407 Processing helix chain 'B' and resid 422 through 437 removed outlier: 3.533A pdb=" N ALA B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 458 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 505 through 517 removed outlier: 4.180A pdb=" N HIS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.538A pdb=" N VAL B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 150 through 155 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 187 through 190 Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 205 through 222 removed outlier: 3.594A pdb=" N ALA C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 240 removed outlier: 3.511A pdb=" N GLU C 231 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU C 236 " --> pdb=" O HIS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 255 removed outlier: 6.028A pdb=" N VAL C 249 " --> pdb=" O ASN C 246 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 250 " --> pdb=" O ASN C 247 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 254 " --> pdb=" O ASP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 297 through 319 removed outlier: 4.078A pdb=" N GLY C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 340 removed outlier: 4.239A pdb=" N VAL C 325 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR C 328 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU C 329 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 331 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 332 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C 340 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 360 removed outlier: 6.418A pdb=" N VAL C 350 " --> pdb=" O TYR C 347 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 360 " --> pdb=" O PHE C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 388 through 396 Processing helix chain 'C' and resid 406 through 417 removed outlier: 6.841A pdb=" N LEU C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE C 413 " --> pdb=" O THR C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 424 No H-bonds generated for 'chain 'C' and resid 421 through 424' Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 116 through 119 No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 126 through 143 Processing helix chain 'D' and resid 150 through 158 removed outlier: 4.183A pdb=" N VAL D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'D' and resid 209 through 222 Processing helix chain 'D' and resid 228 through 240 removed outlier: 3.600A pdb=" N GLN D 234 " --> pdb=" O GLU D 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS D 240 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 255 removed outlier: 6.024A pdb=" N VAL D 249 " --> pdb=" O ASN D 246 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE D 252 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 297 through 319 Processing helix chain 'D' and resid 325 through 340 removed outlier: 4.687A pdb=" N LEU D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 360 removed outlier: 6.219A pdb=" N VAL D 350 " --> pdb=" O TYR D 347 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 351 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 359 " --> pdb=" O GLY D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 396 Processing helix chain 'D' and resid 410 through 413 No H-bonds generated for 'chain 'D' and resid 410 through 413' Processing helix chain 'D' and resid 421 through 424 No H-bonds generated for 'chain 'D' and resid 421 through 424' Processing helix chain 'E' and resid 13 through 23 Processing helix chain 'E' and resid 34 through 41 Processing helix chain 'E' and resid 57 through 60 No H-bonds generated for 'chain 'E' and resid 57 through 60' Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 75 through 78 No H-bonds generated for 'chain 'E' and resid 75 through 78' Processing helix chain 'E' and resid 99 through 109 removed outlier: 3.672A pdb=" N SER E 103 " --> pdb=" O PRO E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 removed outlier: 3.754A pdb=" N GLN E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 212 Processing helix chain 'E' and resid 227 through 245 Processing helix chain 'F' and resid 13 through 23 Processing helix chain 'F' and resid 34 through 41 Processing helix chain 'F' and resid 66 through 70 Processing helix chain 'F' and resid 74 through 79 Processing helix chain 'F' and resid 99 through 109 Processing helix chain 'F' and resid 128 through 140 removed outlier: 4.258A pdb=" N GLN F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 212 removed outlier: 3.613A pdb=" N ALA F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 206 through 212' Processing helix chain 'F' and resid 227 through 245 Processing helix chain 'X' and resid 24 through 35 removed outlier: 5.245A pdb=" N LYS X 29 " --> pdb=" O GLU X 25 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR X 35 " --> pdb=" O ILE X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 95 through 108 removed outlier: 4.249A pdb=" N GLU X 99 " --> pdb=" O GLU X 96 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS X 100 " --> pdb=" O THR X 97 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL X 101 " --> pdb=" O LYS X 98 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL X 104 " --> pdb=" O VAL X 101 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS X 105 " --> pdb=" O ARG X 102 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS X 107 " --> pdb=" O VAL X 104 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET X 108 " --> pdb=" O CYS X 105 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 118 through 122 removed outlier: 3.529A pdb=" N TYR A 176 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 118 through 122 removed outlier: 3.671A pdb=" N TYR B 176 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.093A pdb=" N SER C 108 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 99 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 279 through 284 removed outlier: 6.814A pdb=" N PHE C 291 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 42 through 46 Processing sheet with id= F, first strand: chain 'D' and resid 279 through 284 removed outlier: 7.167A pdb=" N PHE D 291 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 83 through 89 Processing sheet with id= H, first strand: chain 'E' and resid 183 through 185 removed outlier: 3.784A pdb=" N GLY E 201 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET E 185 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASN E 199 " --> pdb=" O MET E 185 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 83 through 86 Processing sheet with id= J, first strand: chain 'F' and resid 177 through 179 removed outlier: 3.591A pdb=" N GLY F 201 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET F 185 " --> pdb=" O ASN F 199 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASN F 199 " --> pdb=" O MET F 185 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'X' and resid 113 through 117 removed outlier: 4.453A pdb=" N ARG X 116 " --> pdb=" O GLU X 15 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU X 15 " --> pdb=" O ARG X 116 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE X 92 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG X 42 " --> pdb=" O GLU X 91 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 1854 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: 5.31 Time building geometry restraints manager: 7.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5378 1.33 - 1.45: 3635 1.45 - 1.58: 9449 1.58 - 1.70: 0 1.70 - 1.82: 195 Bond restraints: 18657 Sorted by residual: bond pdb=" CA LEU A 171 " pdb=" C LEU A 171 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.29e-02 6.01e+03 1.14e+01 bond pdb=" CG1 ILE C 266 " pdb=" CD1 ILE C 266 " ideal model delta sigma weight residual 1.513 1.383 0.130 3.90e-02 6.57e+02 1.11e+01 bond pdb=" CA ILE B 355 " pdb=" C ILE B 355 " ideal model delta sigma weight residual 1.524 1.481 0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" CA ASP A 173 " pdb=" C ASP A 173 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.34e-02 5.57e+03 1.03e+01 bond pdb=" CA PRO B 409 " pdb=" C PRO B 409 " ideal model delta sigma weight residual 1.528 1.500 0.029 9.10e-03 1.21e+04 9.99e+00 ... (remaining 18652 not shown) Histogram of bond angle deviations from ideal: 94.62 - 102.66: 121 102.66 - 110.70: 5665 110.70 - 118.74: 9104 118.74 - 126.78: 10182 126.78 - 134.81: 199 Bond angle restraints: 25271 Sorted by residual: angle pdb=" N GLN B 161 " pdb=" CA GLN B 161 " pdb=" C GLN B 161 " ideal model delta sigma weight residual 109.39 122.02 -12.63 1.59e+00 3.96e-01 6.30e+01 angle pdb=" N SER B 419 " pdb=" CA SER B 419 " pdb=" C SER B 419 " ideal model delta sigma weight residual 109.52 97.25 12.27 1.55e+00 4.16e-01 6.27e+01 angle pdb=" N GLU B 162 " pdb=" CA GLU B 162 " pdb=" C GLU B 162 " ideal model delta sigma weight residual 109.72 97.12 12.60 1.60e+00 3.91e-01 6.20e+01 angle pdb=" N LEU B 100 " pdb=" CA LEU B 100 " pdb=" C LEU B 100 " ideal model delta sigma weight residual 112.59 103.05 9.54 1.22e+00 6.72e-01 6.11e+01 angle pdb=" N GLN B 420 " pdb=" CA GLN B 420 " pdb=" C GLN B 420 " ideal model delta sigma weight residual 112.24 104.09 8.15 1.28e+00 6.10e-01 4.05e+01 ... (remaining 25266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10045 17.97 - 35.94: 928 35.94 - 53.91: 120 53.91 - 71.89: 25 71.89 - 89.86: 13 Dihedral angle restraints: 11131 sinusoidal: 4267 harmonic: 6864 Sorted by residual: dihedral pdb=" C ASP B 353 " pdb=" N ASP B 353 " pdb=" CA ASP B 353 " pdb=" CB ASP B 353 " ideal model delta harmonic sigma weight residual -122.60 -137.73 15.13 0 2.50e+00 1.60e-01 3.66e+01 dihedral pdb=" N ASP B 353 " pdb=" C ASP B 353 " pdb=" CA ASP B 353 " pdb=" CB ASP B 353 " ideal model delta harmonic sigma weight residual 122.80 137.61 -14.81 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" CA PHE D 143 " pdb=" C PHE D 143 " pdb=" N GLY D 144 " pdb=" CA GLY D 144 " ideal model delta harmonic sigma weight residual -180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 11128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2649 0.132 - 0.263: 130 0.263 - 0.395: 11 0.395 - 0.526: 5 0.526 - 0.658: 3 Chirality restraints: 2798 Sorted by residual: chirality pdb=" CA ASP B 353 " pdb=" N ASP B 353 " pdb=" C ASP B 353 " pdb=" CB ASP B 353 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA ASP B 354 " pdb=" N ASP B 354 " pdb=" C ASP B 354 " pdb=" CB ASP B 354 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CA GLN B 161 " pdb=" N GLN B 161 " pdb=" C GLN B 161 " pdb=" CB GLN B 161 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.55 2.00e-01 2.50e+01 7.43e+00 ... (remaining 2795 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 498 " 0.022 2.00e-02 2.50e+03 3.22e-02 2.07e+01 pdb=" CG TYR A 498 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 498 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 498 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 498 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 498 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 498 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 498 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 408 " -0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 409 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 104 " -0.012 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR E 104 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR E 104 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 104 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR E 104 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 104 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 104 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 104 " 0.001 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 275 2.59 - 3.17: 15785 3.17 - 3.75: 31288 3.75 - 4.32: 43966 4.32 - 4.90: 71678 Nonbonded interactions: 162992 Sorted by model distance: nonbonded pdb=" O SER B 419 " pdb=" CD GLN B 420 " model vdw 2.014 3.270 nonbonded pdb=" O SER B 419 " pdb=" OE1 GLN B 420 " model vdw 2.068 3.040 nonbonded pdb=" C SER B 419 " pdb=" OE1 GLN B 420 " model vdw 2.172 3.270 nonbonded pdb=" OG SER E 103 " pdb=" NE2 GLN E 122 " model vdw 2.193 2.520 nonbonded pdb=" O SER C 326 " pdb=" OG SER C 358 " model vdw 2.212 2.440 ... (remaining 162987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 92 through 158 or resid 167 through 569)) } ncs_group { reference = (chain 'C' and resid 2 through 432) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.390 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 49.100 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.010 0.130 18657 Z= 0.632 Angle : 1.103 12.625 25271 Z= 0.621 Chirality : 0.071 0.658 2798 Planarity : 0.007 0.086 3348 Dihedral : 13.995 89.856 6767 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.32 % Allowed : 1.06 % Favored : 98.62 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.08 % 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: -2.33 (0.15), residues: 2384 helix: -1.43 (0.13), residues: 1153 sheet: -1.50 (0.42), residues: 138 loop : -1.55 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 447 HIS 0.016 0.002 HIS B 127 PHE 0.051 0.004 PHE C 360 TYR 0.073 0.004 TYR A 498 ARG 0.012 0.001 ARG E 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 210 time to evaluate : 2.133 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.8557 (pmm) cc_final: 0.8236 (pmm) REVERT: F 168 VAL cc_start: 0.8862 (t) cc_final: 0.8497 (m) outliers start: 6 outliers final: 1 residues processed: 216 average time/residue: 0.3253 time to fit residues: 104.9312 Evaluate side-chains 137 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 ASN C 324 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN E 87 GLN F 54 HIS F 220 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18657 Z= 0.187 Angle : 0.581 6.797 25271 Z= 0.308 Chirality : 0.042 0.158 2798 Planarity : 0.005 0.064 3348 Dihedral : 5.605 54.551 2628 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.79 % Allowed : 7.89 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.31 (0.16), residues: 2384 helix: -0.38 (0.15), residues: 1173 sheet: -1.33 (0.41), residues: 145 loop : -1.26 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 447 HIS 0.008 0.001 HIS E 159 PHE 0.015 0.002 PHE F 101 TYR 0.023 0.002 TYR D 365 ARG 0.005 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 2.093 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 154 MET cc_start: 0.6354 (tpp) cc_final: 0.6130 (mmp) REVERT: A 500 MET cc_start: 0.8526 (pmm) cc_final: 0.7981 (pmm) REVERT: A 558 MET cc_start: 0.7472 (tpp) cc_final: 0.7257 (tpp) REVERT: C 59 MET cc_start: 0.7873 (ptp) cc_final: 0.7559 (ptm) REVERT: C 125 MET cc_start: 0.7449 (mmm) cc_final: 0.7075 (mmm) REVERT: C 142 MET cc_start: 0.7466 (ppp) cc_final: 0.7212 (ppp) REVERT: D 125 MET cc_start: 0.8075 (ppp) cc_final: 0.7857 (ptm) REVERT: F 220 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8181 (t0) REVERT: X 63 LYS cc_start: 0.7907 (tppt) cc_final: 0.7399 (tppt) outliers start: 15 outliers final: 3 residues processed: 164 average time/residue: 0.2821 time to fit residues: 73.6641 Evaluate side-chains 132 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain F residue 220 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 0.5980 chunk 235 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 220 GLN C 234 GLN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN D 171 ASN D 173 GLN D 180 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 18657 Z= 0.511 Angle : 0.726 8.061 25271 Z= 0.385 Chirality : 0.047 0.194 2798 Planarity : 0.005 0.060 3348 Dihedral : 5.671 58.862 2628 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.75 % Allowed : 11.43 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.06 (0.17), residues: 2384 helix: -0.12 (0.15), residues: 1197 sheet: -1.50 (0.40), residues: 143 loop : -1.17 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 447 HIS 0.008 0.001 HIS E 159 PHE 0.025 0.002 PHE E 105 TYR 0.031 0.002 TYR C 331 ARG 0.012 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 2.168 Fit side-chains REVERT: A 111 MET cc_start: 0.8382 (ttp) cc_final: 0.8157 (ttt) REVERT: A 128 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7766 (tm-30) REVERT: A 247 MET cc_start: 0.7975 (mtt) cc_final: 0.7726 (mtt) REVERT: A 500 MET cc_start: 0.8619 (pmm) cc_final: 0.7754 (pmm) REVERT: A 558 MET cc_start: 0.7588 (tpp) cc_final: 0.7322 (tpp) REVERT: C 59 MET cc_start: 0.7971 (ptp) cc_final: 0.7761 (ptm) REVERT: C 125 MET cc_start: 0.7987 (mmm) cc_final: 0.7674 (mmm) REVERT: D 22 MET cc_start: 0.8469 (mmp) cc_final: 0.8117 (mmm) REVERT: X 63 LYS cc_start: 0.7989 (tppt) cc_final: 0.7420 (tppt) outliers start: 33 outliers final: 16 residues processed: 150 average time/residue: 0.3159 time to fit residues: 75.2001 Evaluate side-chains 132 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.0170 chunk 164 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 146 optimal weight: 0.0970 chunk 219 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18657 Z= 0.190 Angle : 0.545 7.458 25271 Z= 0.284 Chirality : 0.042 0.165 2798 Planarity : 0.004 0.057 3348 Dihedral : 5.159 51.297 2628 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.64 % Allowed : 12.39 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.57 (0.17), residues: 2384 helix: 0.32 (0.15), residues: 1181 sheet: -1.37 (0.42), residues: 138 loop : -0.96 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 447 HIS 0.005 0.001 HIS E 159 PHE 0.015 0.002 PHE A 549 TYR 0.016 0.001 TYR D 365 ARG 0.005 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 2.101 Fit side-chains REVERT: A 111 MET cc_start: 0.8227 (ttp) cc_final: 0.8001 (ttt) REVERT: A 128 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 500 MET cc_start: 0.8587 (pmm) cc_final: 0.7698 (pmm) REVERT: A 558 MET cc_start: 0.7706 (tpp) cc_final: 0.7382 (tpp) REVERT: B 494 ASN cc_start: 0.8956 (t0) cc_final: 0.8615 (t0) REVERT: C 125 MET cc_start: 0.7702 (mmm) cc_final: 0.7456 (mmm) REVERT: D 22 MET cc_start: 0.8546 (mmp) cc_final: 0.8303 (mmm) outliers start: 31 outliers final: 14 residues processed: 156 average time/residue: 0.2878 time to fit residues: 73.0515 Evaluate side-chains 133 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 315 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS F 138 GLN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18657 Z= 0.263 Angle : 0.555 6.318 25271 Z= 0.291 Chirality : 0.042 0.187 2798 Planarity : 0.004 0.054 3348 Dihedral : 5.024 53.193 2628 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.96 % Allowed : 13.39 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.34 (0.17), residues: 2384 helix: 0.54 (0.16), residues: 1178 sheet: -1.29 (0.43), residues: 139 loop : -0.88 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 447 HIS 0.004 0.001 HIS E 159 PHE 0.018 0.001 PHE E 101 TYR 0.017 0.002 TYR C 215 ARG 0.009 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 2.060 Fit side-chains REVERT: A 128 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 500 MET cc_start: 0.8611 (pmm) cc_final: 0.7718 (pmm) REVERT: A 558 MET cc_start: 0.7804 (tpp) cc_final: 0.7376 (tpp) REVERT: B 108 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7170 (mmm) REVERT: B 494 ASN cc_start: 0.8978 (t0) cc_final: 0.8664 (t0) REVERT: C 125 MET cc_start: 0.7796 (mmm) cc_final: 0.7559 (mmm) REVERT: X 28 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: X 63 LYS cc_start: 0.8034 (tppt) cc_final: 0.7510 (tppt) outliers start: 37 outliers final: 28 residues processed: 153 average time/residue: 0.2669 time to fit residues: 66.3223 Evaluate side-chains 152 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 28 GLN Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 232 optimal weight: 0.0370 chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS X 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18657 Z= 0.179 Angle : 0.517 6.133 25271 Z= 0.269 Chirality : 0.041 0.177 2798 Planarity : 0.004 0.057 3348 Dihedral : 4.834 53.299 2628 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.91 % Allowed : 14.66 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.16 (0.18), residues: 2384 helix: 0.72 (0.16), residues: 1176 sheet: -1.09 (0.43), residues: 144 loop : -0.83 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 447 HIS 0.003 0.001 HIS E 159 PHE 0.015 0.001 PHE E 105 TYR 0.016 0.001 TYR C 215 ARG 0.009 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 2.051 Fit side-chains REVERT: A 128 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7835 (tm-30) REVERT: A 500 MET cc_start: 0.8598 (pmm) cc_final: 0.7698 (pmm) REVERT: A 558 MET cc_start: 0.7794 (tpp) cc_final: 0.7365 (tpp) REVERT: B 108 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7241 (mmm) REVERT: B 255 MET cc_start: 0.8152 (mpp) cc_final: 0.7723 (mpp) REVERT: B 494 ASN cc_start: 0.8951 (t0) cc_final: 0.8646 (t0) REVERT: C 125 MET cc_start: 0.7693 (mmm) cc_final: 0.7478 (mmm) REVERT: D 22 MET cc_start: 0.8679 (mmp) cc_final: 0.8416 (mmm) REVERT: X 63 LYS cc_start: 0.8035 (tppt) cc_final: 0.7505 (tppt) outliers start: 36 outliers final: 23 residues processed: 162 average time/residue: 0.2779 time to fit residues: 72.5270 Evaluate side-chains 144 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 28 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 129 optimal weight: 0.5980 chunk 231 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 141 optimal weight: 0.0020 chunk 106 optimal weight: 8.9990 overall best weight: 2.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18657 Z= 0.224 Angle : 0.537 8.577 25271 Z= 0.278 Chirality : 0.042 0.178 2798 Planarity : 0.004 0.055 3348 Dihedral : 4.785 54.317 2628 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.96 % Allowed : 15.03 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.02 (0.18), residues: 2384 helix: 0.86 (0.16), residues: 1162 sheet: -1.08 (0.44), residues: 141 loop : -0.77 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 447 HIS 0.003 0.001 HIS E 159 PHE 0.020 0.002 PHE E 105 TYR 0.017 0.001 TYR C 215 ARG 0.010 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 2.184 Fit side-chains REVERT: A 500 MET cc_start: 0.8545 (pmm) cc_final: 0.7664 (pmm) REVERT: A 558 MET cc_start: 0.7913 (tpp) cc_final: 0.7478 (tpp) REVERT: B 108 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7168 (mmm) REVERT: B 255 MET cc_start: 0.8176 (mpp) cc_final: 0.7655 (mpp) REVERT: B 494 ASN cc_start: 0.8941 (t0) cc_final: 0.8631 (t0) REVERT: C 125 MET cc_start: 0.7805 (mmm) cc_final: 0.7587 (mmm) REVERT: C 168 MET cc_start: 0.8514 (ptp) cc_final: 0.8309 (ptp) REVERT: D 22 MET cc_start: 0.8632 (mmp) cc_final: 0.8369 (mmm) REVERT: X 28 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: X 63 LYS cc_start: 0.8098 (tppt) cc_final: 0.7582 (tppt) outliers start: 37 outliers final: 30 residues processed: 156 average time/residue: 0.2693 time to fit residues: 68.3627 Evaluate side-chains 150 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 28 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 157 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18657 Z= 0.228 Angle : 0.544 8.085 25271 Z= 0.281 Chirality : 0.042 0.178 2798 Planarity : 0.004 0.056 3348 Dihedral : 4.770 54.404 2628 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.22 % Allowed : 15.62 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.02 (0.18), residues: 2384 helix: 0.89 (0.16), residues: 1163 sheet: -1.11 (0.45), residues: 139 loop : -0.74 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 447 HIS 0.003 0.001 HIS E 159 PHE 0.027 0.001 PHE A 549 TYR 0.018 0.001 TYR C 215 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 2.255 Fit side-chains REVERT: A 500 MET cc_start: 0.8529 (pmm) cc_final: 0.7666 (pmm) REVERT: A 558 MET cc_start: 0.7888 (tpp) cc_final: 0.7469 (tpp) REVERT: B 108 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7283 (mmm) REVERT: B 255 MET cc_start: 0.8167 (mpp) cc_final: 0.7634 (mpp) REVERT: B 494 ASN cc_start: 0.8936 (t0) cc_final: 0.8634 (t0) REVERT: D 22 MET cc_start: 0.8635 (mmp) cc_final: 0.8376 (mmm) REVERT: X 28 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: X 63 LYS cc_start: 0.8116 (tppt) cc_final: 0.7577 (tppt) outliers start: 42 outliers final: 34 residues processed: 160 average time/residue: 0.2962 time to fit residues: 78.1989 Evaluate side-chains 156 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 28 GLN Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.8980 chunk 221 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18657 Z= 0.181 Angle : 0.536 13.009 25271 Z= 0.273 Chirality : 0.041 0.176 2798 Planarity : 0.004 0.057 3348 Dihedral : 4.686 54.385 2628 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.96 % Allowed : 15.99 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.10 (0.18), residues: 2384 helix: 0.94 (0.16), residues: 1163 sheet: -1.00 (0.44), residues: 144 loop : -0.70 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 447 HIS 0.003 0.001 HIS E 159 PHE 0.023 0.001 PHE A 549 TYR 0.018 0.001 TYR C 215 ARG 0.013 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 1.962 Fit side-chains REVERT: A 280 MET cc_start: 0.8680 (mpp) cc_final: 0.8480 (mmm) REVERT: A 284 ARG cc_start: 0.8609 (mmm160) cc_final: 0.8375 (ttt180) REVERT: A 558 MET cc_start: 0.7882 (tpp) cc_final: 0.7426 (tpp) REVERT: B 108 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7335 (mmm) REVERT: B 255 MET cc_start: 0.8129 (mpp) cc_final: 0.7666 (mtm) REVERT: B 494 ASN cc_start: 0.8924 (t0) cc_final: 0.8645 (t0) REVERT: D 22 MET cc_start: 0.8645 (mmp) cc_final: 0.8382 (mmm) REVERT: X 28 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7924 (pm20) outliers start: 37 outliers final: 31 residues processed: 157 average time/residue: 0.2660 time to fit residues: 68.0566 Evaluate side-chains 152 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain X residue 28 GLN Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 0.0010 chunk 108 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 239 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN D 180 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18657 Z= 0.149 Angle : 0.522 8.917 25271 Z= 0.266 Chirality : 0.041 0.169 2798 Planarity : 0.004 0.057 3348 Dihedral : 4.558 55.149 2628 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.64 % Allowed : 16.20 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.24 (0.18), residues: 2384 helix: 1.06 (0.16), residues: 1163 sheet: -0.81 (0.45), residues: 144 loop : -0.65 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 447 HIS 0.003 0.001 HIS B 223 PHE 0.026 0.001 PHE E 105 TYR 0.017 0.001 TYR C 215 ARG 0.010 0.000 ARG A 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 2.040 Fit side-chains REVERT: A 284 ARG cc_start: 0.8543 (mmm160) cc_final: 0.8336 (ttt180) REVERT: A 558 MET cc_start: 0.7883 (tpp) cc_final: 0.7408 (tpp) REVERT: B 108 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7356 (mmm) REVERT: B 255 MET cc_start: 0.8055 (mpp) cc_final: 0.7497 (mtm) REVERT: B 494 ASN cc_start: 0.8902 (t0) cc_final: 0.8645 (t0) REVERT: D 22 MET cc_start: 0.8657 (mmp) cc_final: 0.8374 (mmm) REVERT: X 28 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: X 63 LYS cc_start: 0.8046 (tppt) cc_final: 0.7498 (tppt) outliers start: 31 outliers final: 21 residues processed: 156 average time/residue: 0.2708 time to fit residues: 68.8400 Evaluate side-chains 147 residues out of total 1889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 28 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 195 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.068212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058486 restraints weight = 68718.074| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.47 r_work: 0.3044 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18657 Z= 0.269 Angle : 0.559 8.806 25271 Z= 0.287 Chirality : 0.042 0.174 2798 Planarity : 0.004 0.055 3348 Dihedral : 4.660 55.546 2628 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.54 % Allowed : 16.25 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.22 (0.18), residues: 2384 helix: 1.03 (0.16), residues: 1161 sheet: -0.94 (0.44), residues: 144 loop : -0.62 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 447 HIS 0.004 0.001 HIS E 159 PHE 0.032 0.002 PHE A 549 TYR 0.026 0.001 TYR C 215 ARG 0.010 0.000 ARG A 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3161.41 seconds wall clock time: 59 minutes 23.31 seconds (3563.31 seconds total)