Starting phenix.real_space_refine on Sat Jan 20 05:53:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/01_2024/8t1o_40973_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/01_2024/8t1o_40973.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/01_2024/8t1o_40973_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/01_2024/8t1o_40973_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/01_2024/8t1o_40973_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/01_2024/8t1o_40973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/01_2024/8t1o_40973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/01_2024/8t1o_40973_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/01_2024/8t1o_40973_updated.pdb" } resolution = 3.3 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= 1.211 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 3 5.49 5 S 72 5.16 5 C 8811 2.51 5 N 2338 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ASP 573": "OD1" <-> "OD2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B ASP 366": "OD1" <-> "OD2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B ASP 515": "OD1" <-> "OD2" Residue "B TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "M TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M GLU 164": "OE1" <-> "OE2" Residue "M GLU 172": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 260": "OE1" <-> "OE2" Residue "M PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 271": "OE1" <-> "OE2" Residue "M PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 391": "OE1" <-> "OE2" Residue "M TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 408": "OE1" <-> "OE2" Residue "M ASP 415": "OD1" <-> "OD2" Residue "S TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 75": "OD1" <-> "OD2" Residue "S GLU 93": "OE1" <-> "OE2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13800 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4721 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 22, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4518 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 26, 'TRANS': 543} Chain: "M" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3297 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "S" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1190 Classifications: {'peptide': 141} Link IDs: {'TRANS': 140} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-2': 1, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 7.49, per 1000 atoms: 0.54 Number of scatterers: 13800 At special positions: 0 Unit cell: (107.36, 116.16, 125.84, 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 72 16.00 P 3 15.00 O 2576 8.00 N 2338 7.00 C 8811 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: 5.49 Conformation dependent library (CDL) restraints added in 2.7 seconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 7 sheets defined 56.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 26 through 44 Processing helix chain 'A' and resid 52 through 68 Processing helix chain 'A' and resid 76 through 83 Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 141 through 153 removed outlier: 5.399A pdb=" N GLY A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 162 through 178 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 188 through 197 removed outlier: 3.746A pdb=" N LEU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.546A pdb=" N VAL A 226 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 237 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 274 through 291 removed outlier: 3.882A pdb=" N ALA A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 320 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.537A pdb=" N VAL A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.702A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 379 removed outlier: 4.149A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N THR A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 402 through 415 removed outlier: 3.691A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 434 removed outlier: 4.166A pdb=" N GLU A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.717A pdb=" N VAL A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.937A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 494 through 507 removed outlier: 3.645A pdb=" N GLU A 506 " --> pdb=" O TYR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 530 Processing helix chain 'A' and resid 535 through 551 Processing helix chain 'A' and resid 553 through 563 removed outlier: 4.789A pdb=" N ALA A 557 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 558 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 563 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'B' and resid 14 through 22 Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 48 through 58 Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 63 through 77 Processing helix chain 'B' and resid 85 through 96 removed outlier: 3.573A pdb=" N GLU B 96 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.943A pdb=" N GLU B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix Processing helix chain 'B' and resid 135 through 150 Processing helix chain 'B' and resid 156 through 169 removed outlier: 3.549A pdb=" N ILE B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 189 removed outlier: 4.285A pdb=" N GLU B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 213 removed outlier: 4.680A pdb=" N ASN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 228 removed outlier: 3.530A pdb=" N ILE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 248 removed outlier: 3.510A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 253 through 265 Processing helix chain 'B' and resid 275 through 293 removed outlier: 4.137A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 4.023A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.679A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.022A pdb=" N THR B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.584A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 400 Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.910A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 434 removed outlier: 4.503A pdb=" N ALA B 430 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 434 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 462 through 472 removed outlier: 3.908A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 494 Processing helix chain 'B' and resid 497 through 511 removed outlier: 3.695A pdb=" N GLN B 500 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU B 501 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B 502 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 532 Processing helix chain 'B' and resid 534 through 541 Processing helix chain 'B' and resid 557 through 565 Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'M' and resid 26 through 35 removed outlier: 3.751A pdb=" N ASP M 30 " --> pdb=" O ARG M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 93 Processing helix chain 'M' and resid 98 through 103 Processing helix chain 'M' and resid 105 through 115 Processing helix chain 'M' and resid 129 through 132 No H-bonds generated for 'chain 'M' and resid 129 through 132' Processing helix chain 'M' and resid 145 through 156 Processing helix chain 'M' and resid 254 through 260 Processing helix chain 'S' and resid 25 through 41 removed outlier: 3.703A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 95 Processing helix chain 'S' and resid 100 through 105 Processing helix chain 'S' and resid 107 through 117 Processing helix chain 'S' and resid 128 through 140 Processing sheet with id= A, first strand: chain 'M' and resid 47 through 49 Processing sheet with id= B, first strand: chain 'M' and resid 419 through 428 removed outlier: 3.612A pdb=" N VAL M 181 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER M 193 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER M 204 " --> pdb=" O GLU M 271 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLU M 271 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP M 245 " --> pdb=" O ARG M 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 183 through 185 removed outlier: 3.762A pdb=" N MET M 185 " --> pdb=" O GLU M 432 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 403 through 407 removed outlier: 3.684A pdb=" N TYR M 403 " --> pdb=" O GLY M 215 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE M 263 " --> pdb=" O PHE M 214 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'M' and resid 287 through 296 removed outlier: 3.585A pdb=" N ARG M 288 " --> pdb=" O LYS M 308 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS M 308 " --> pdb=" O ARG M 288 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE M 290 " --> pdb=" O VAL M 306 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL M 306 " --> pdb=" O ILE M 290 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS M 300 " --> pdb=" O VAL M 296 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL M 303 " --> pdb=" O ALA M 368 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA M 368 " --> pdb=" O VAL M 303 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL M 305 " --> pdb=" O ILE M 366 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE M 366 " --> pdb=" O VAL M 305 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU M 369 " --> pdb=" O GLN M 334 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'M' and resid 387 through 389 removed outlier: 3.614A pdb=" N SER M 387 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE M 320 " --> pdb=" O ILE M 355 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE M 355 " --> pdb=" O ILE M 320 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'S' and resid 49 through 52 removed outlier: 3.522A pdb=" N PHE S 52 " --> pdb=" O PHE S 55 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE S 55 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE S 4 " --> pdb=" O CYS S 70 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 1968 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: 4.33 Time building geometry restraints manager: 5.90 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: 4511 1.34 - 1.46: 2734 1.46 - 1.58: 6683 1.58 - 1.70: 4 1.70 - 1.81: 111 Bond restraints: 14043 Sorted by residual: bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.19e-02 7.06e+03 2.40e+00 bond pdb=" CB VAL A 483 " pdb=" CG1 VAL A 483 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.35e+00 bond pdb=" CG GLU S 33 " pdb=" CD GLU S 33 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.35e+00 bond pdb=" CD GLU S 33 " pdb=" OE1 GLU S 33 " ideal model delta sigma weight residual 1.249 1.229 0.020 1.90e-02 2.77e+03 1.14e+00 bond pdb=" CB VAL S 98 " pdb=" CG2 VAL S 98 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.25e-01 ... (remaining 14038 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.71: 329 106.71 - 113.53: 7930 113.53 - 120.35: 5236 120.35 - 127.16: 5412 127.16 - 133.98: 111 Bond angle restraints: 19018 Sorted by residual: angle pdb=" C GLU M 125 " pdb=" N THR M 126 " pdb=" CA THR M 126 " ideal model delta sigma weight residual 121.54 128.70 -7.16 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C GLN A 266 " pdb=" N CYS A 267 " pdb=" CA CYS A 267 " ideal model delta sigma weight residual 122.31 115.52 6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N GLU S 33 " pdb=" CA GLU S 33 " pdb=" CB GLU S 33 " ideal model delta sigma weight residual 110.28 115.29 -5.01 1.55e+00 4.16e-01 1.05e+01 angle pdb=" N HIS B 250 " pdb=" CA HIS B 250 " pdb=" C HIS B 250 " ideal model delta sigma weight residual 108.63 113.72 -5.09 1.60e+00 3.91e-01 1.01e+01 angle pdb=" CA GLN M 154 " pdb=" CB GLN M 154 " pdb=" CG GLN M 154 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 ... (remaining 19013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7756 17.94 - 35.87: 709 35.87 - 53.81: 110 53.81 - 71.74: 28 71.74 - 89.68: 24 Dihedral angle restraints: 8627 sinusoidal: 3508 harmonic: 5119 Sorted by residual: dihedral pdb=" CA HIS B 250 " pdb=" C HIS B 250 " pdb=" N ALA B 251 " pdb=" CA ALA B 251 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA LEU B 196 " pdb=" C LEU B 196 " pdb=" N LEU B 197 " pdb=" CA LEU B 197 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO B 81 " pdb=" C PRO B 81 " pdb=" N ASP B 82 " pdb=" CA ASP B 82 " ideal model delta harmonic sigma weight residual 180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 8624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1454 0.034 - 0.068: 567 0.068 - 0.103: 133 0.103 - 0.137: 58 0.137 - 0.171: 3 Chirality restraints: 2215 Sorted by residual: chirality pdb=" CA GLU S 33 " pdb=" N GLU S 33 " pdb=" C GLU S 33 " pdb=" CB GLU S 33 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA PRO B 201 " pdb=" N PRO B 201 " pdb=" C PRO B 201 " pdb=" CB PRO B 201 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2212 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN S 29 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C GLN S 29 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN S 29 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS S 30 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 124 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO A 125 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 270 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO B 271 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 271 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 271 " -0.023 5.00e-02 4.00e+02 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 260 2.70 - 3.25: 14147 3.25 - 3.80: 21479 3.80 - 4.35: 27804 4.35 - 4.90: 46738 Nonbonded interactions: 110428 Sorted by model distance: nonbonded pdb=" O LEU B 398 " pdb=" OG1 THR B 401 " model vdw 2.146 2.440 nonbonded pdb=" O LEU B 270 " pdb=" OG SER B 274 " model vdw 2.160 2.440 nonbonded pdb=" ND2 ASN B 200 " pdb=" OE1 GLN B 202 " model vdw 2.162 2.520 nonbonded pdb=" OH TYR A 95 " pdb=" OD2 ASP A 119 " model vdw 2.173 2.440 nonbonded pdb=" O ILE A 511 " pdb=" OG SER A 517 " model vdw 2.190 2.440 ... (remaining 110423 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: 3.740 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: 12.570 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 39.830 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 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 : 0.003 0.038 14043 Z= 0.215 Angle : 0.588 8.659 19018 Z= 0.317 Chirality : 0.041 0.171 2215 Planarity : 0.004 0.045 2418 Dihedral : 14.782 89.676 5291 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1712 helix: 1.38 (0.16), residues: 992 sheet: 0.66 (0.38), residues: 165 loop : -0.73 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 462 HIS 0.006 0.001 HIS A 531 PHE 0.016 0.001 PHE A 147 TYR 0.029 0.001 TYR B 70 ARG 0.010 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7273 (t0) cc_final: 0.6994 (t0) REVERT: B 163 ASP cc_start: 0.7423 (p0) cc_final: 0.6855 (t0) REVERT: M 114 GLU cc_start: 0.7137 (tp30) cc_final: 0.6903 (tp30) REVERT: M 158 GLN cc_start: 0.7118 (tm-30) cc_final: 0.6836 (tp40) REVERT: M 410 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7911 (tptm) REVERT: S 33 GLU cc_start: 0.7345 (mp0) cc_final: 0.7066 (mp0) REVERT: S 137 MET cc_start: 0.7017 (tmm) cc_final: 0.6341 (tmm) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2752 time to fit residues: 85.5156 Evaluate side-chains 176 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 81 optimal weight: 0.1980 chunk 99 optimal weight: 0.6980 chunk 155 optimal weight: 0.0670 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 24 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 318 GLN S 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14043 Z= 0.165 Angle : 0.515 7.587 19018 Z= 0.272 Chirality : 0.040 0.147 2215 Planarity : 0.004 0.036 2418 Dihedral : 4.509 57.507 1884 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 0.65 % Allowed : 6.58 % Favored : 92.76 % 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: 0.94 (0.20), residues: 1712 helix: 1.37 (0.16), residues: 996 sheet: 0.84 (0.38), residues: 166 loop : -0.75 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 462 HIS 0.005 0.001 HIS A 531 PHE 0.013 0.001 PHE M 81 TYR 0.020 0.001 TYR B 70 ARG 0.005 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7234 (t0) cc_final: 0.6927 (t0) REVERT: A 371 GLU cc_start: 0.6998 (tp30) cc_final: 0.6733 (tp30) REVERT: B 163 ASP cc_start: 0.7573 (p0) cc_final: 0.6896 (t0) REVERT: B 315 GLU cc_start: 0.7923 (pm20) cc_final: 0.7474 (pm20) REVERT: M 361 MET cc_start: 0.4873 (mtm) cc_final: 0.4525 (mtm) REVERT: M 410 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7815 (tptm) REVERT: S 33 GLU cc_start: 0.7518 (mp0) cc_final: 0.7097 (mp0) outliers start: 10 outliers final: 6 residues processed: 194 average time/residue: 0.2689 time to fit residues: 75.7189 Evaluate side-chains 186 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 152 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 105 optimal weight: 0.0030 chunk 42 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 chunk 168 optimal weight: 0.5980 chunk 138 optimal weight: 0.0570 chunk 154 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 173 ASN M 148 GLN M 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14043 Z= 0.152 Angle : 0.489 6.664 19018 Z= 0.258 Chirality : 0.039 0.188 2215 Planarity : 0.004 0.036 2418 Dihedral : 4.388 59.088 1884 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.85 % Allowed : 8.93 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1712 helix: 1.47 (0.16), residues: 993 sheet: 0.73 (0.38), residues: 170 loop : -0.80 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 462 HIS 0.004 0.001 HIS A 531 PHE 0.012 0.001 PHE A 361 TYR 0.018 0.001 TYR B 70 ARG 0.003 0.000 ARG S 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7240 (t0) cc_final: 0.6919 (t0) REVERT: B 163 ASP cc_start: 0.7599 (p0) cc_final: 0.6910 (t0) REVERT: M 185 MET cc_start: 0.5989 (ppp) cc_final: 0.5761 (tmm) REVERT: M 410 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7846 (tptm) REVERT: S 46 HIS cc_start: 0.7434 (m170) cc_final: 0.7232 (m-70) outliers start: 13 outliers final: 7 residues processed: 194 average time/residue: 0.2795 time to fit residues: 79.4395 Evaluate side-chains 182 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain S residue 54 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 0.0040 chunk 74 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 165 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14043 Z= 0.163 Angle : 0.477 6.511 19018 Z= 0.250 Chirality : 0.039 0.141 2215 Planarity : 0.003 0.035 2418 Dihedral : 4.278 59.245 1884 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 1.11 % Allowed : 9.91 % Favored : 88.98 % 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: 1.02 (0.20), residues: 1712 helix: 1.50 (0.16), residues: 993 sheet: 0.76 (0.38), residues: 166 loop : -0.81 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 462 HIS 0.004 0.001 HIS M 10 PHE 0.010 0.001 PHE S 4 TYR 0.017 0.001 TYR B 70 ARG 0.002 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 1.636 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7197 (t0) cc_final: 0.6867 (t0) REVERT: A 223 LYS cc_start: 0.6650 (ttpt) cc_final: 0.5626 (tptt) REVERT: B 121 TYR cc_start: 0.7163 (m-80) cc_final: 0.6836 (m-80) REVERT: B 163 ASP cc_start: 0.7628 (p0) cc_final: 0.6924 (t0) REVERT: M 410 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7829 (tptm) outliers start: 17 outliers final: 11 residues processed: 188 average time/residue: 0.2689 time to fit residues: 74.3524 Evaluate side-chains 191 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain S residue 54 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 123 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14043 Z= 0.170 Angle : 0.479 5.982 19018 Z= 0.251 Chirality : 0.039 0.140 2215 Planarity : 0.003 0.035 2418 Dihedral : 4.212 57.689 1884 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 1.43 % Allowed : 10.37 % Favored : 88.20 % 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: 1.06 (0.20), residues: 1712 helix: 1.50 (0.16), residues: 996 sheet: 0.86 (0.39), residues: 166 loop : -0.79 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.003 0.001 HIS A 369 PHE 0.013 0.001 PHE M 394 TYR 0.018 0.001 TYR B 70 ARG 0.002 0.000 ARG B 520 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7191 (t0) cc_final: 0.6860 (t0) REVERT: A 223 LYS cc_start: 0.6709 (ttpt) cc_final: 0.5717 (tptt) REVERT: A 371 GLU cc_start: 0.6986 (tp30) cc_final: 0.6766 (tp30) REVERT: B 163 ASP cc_start: 0.7598 (p0) cc_final: 0.6984 (t0) REVERT: B 184 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7233 (mm) REVERT: B 423 ASN cc_start: 0.8252 (t0) cc_final: 0.8038 (t0) REVERT: M 154 GLN cc_start: 0.7499 (pp30) cc_final: 0.7196 (pp30) REVERT: M 158 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6283 (mt0) REVERT: M 410 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7834 (tptm) REVERT: S 139 GLN cc_start: 0.7463 (tm-30) cc_final: 0.7019 (tm-30) outliers start: 22 outliers final: 14 residues processed: 198 average time/residue: 0.2780 time to fit residues: 79.5952 Evaluate side-chains 187 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 172 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain S residue 54 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 165 optimal weight: 0.1980 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14043 Z= 0.221 Angle : 0.504 5.865 19018 Z= 0.263 Chirality : 0.039 0.149 2215 Planarity : 0.003 0.035 2418 Dihedral : 4.233 56.086 1884 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.63 % Allowed : 11.47 % Favored : 86.90 % 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: 0.97 (0.20), residues: 1712 helix: 1.41 (0.16), residues: 993 sheet: 0.91 (0.40), residues: 166 loop : -0.81 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.004 0.001 HIS B 250 PHE 0.014 0.001 PHE M 394 TYR 0.018 0.001 TYR B 70 ARG 0.002 0.000 ARG B 520 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 175 time to evaluate : 1.682 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7246 (t0) cc_final: 0.6914 (t0) REVERT: A 223 LYS cc_start: 0.6803 (ttpt) cc_final: 0.5834 (tptt) REVERT: A 371 GLU cc_start: 0.7022 (tp30) cc_final: 0.6751 (tp30) REVERT: B 163 ASP cc_start: 0.7529 (p0) cc_final: 0.6958 (t0) REVERT: B 184 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7248 (mm) REVERT: M 108 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8080 (mp) REVERT: M 185 MET cc_start: 0.6338 (ppp) cc_final: 0.6078 (tmm) REVERT: M 203 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7638 (mtmm) REVERT: M 319 LYS cc_start: 0.6689 (tptp) cc_final: 0.6410 (tmtt) REVERT: M 410 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7846 (tptm) outliers start: 25 outliers final: 17 residues processed: 191 average time/residue: 0.2695 time to fit residues: 75.0727 Evaluate side-chains 188 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 120 optimal weight: 0.0000 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 103 optimal weight: 0.0370 chunk 100 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS M 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14043 Z= 0.167 Angle : 0.485 7.793 19018 Z= 0.254 Chirality : 0.039 0.137 2215 Planarity : 0.003 0.035 2418 Dihedral : 4.165 54.891 1884 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 1.83 % Allowed : 12.06 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.20), residues: 1712 helix: 1.52 (0.16), residues: 992 sheet: 0.90 (0.40), residues: 165 loop : -0.81 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 462 HIS 0.003 0.001 HIS A 369 PHE 0.011 0.001 PHE S 4 TYR 0.021 0.001 TYR B 70 ARG 0.002 0.000 ARG B 520 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 1.650 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7227 (t0) cc_final: 0.6917 (t0) REVERT: A 371 GLU cc_start: 0.6984 (tp30) cc_final: 0.6778 (tp30) REVERT: B 83 MET cc_start: 0.7333 (ppp) cc_final: 0.6799 (ptm) REVERT: B 163 ASP cc_start: 0.7490 (p0) cc_final: 0.6950 (t0) REVERT: B 184 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7230 (mm) REVERT: M 108 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8038 (mp) REVERT: M 185 MET cc_start: 0.6354 (ppp) cc_final: 0.6127 (tmm) REVERT: M 203 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7660 (mtmm) REVERT: M 410 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7827 (tptm) REVERT: S 139 GLN cc_start: 0.7449 (tm-30) cc_final: 0.7009 (tm-30) outliers start: 28 outliers final: 14 residues processed: 196 average time/residue: 0.2697 time to fit residues: 76.9263 Evaluate side-chains 190 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS M 41 GLN M 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14043 Z= 0.223 Angle : 0.511 6.965 19018 Z= 0.267 Chirality : 0.040 0.150 2215 Planarity : 0.004 0.035 2418 Dihedral : 4.195 53.519 1884 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 1.37 % Allowed : 12.65 % Favored : 85.98 % 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: 0.97 (0.20), residues: 1712 helix: 1.44 (0.16), residues: 989 sheet: 0.70 (0.39), residues: 171 loop : -0.79 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.004 0.001 HIS B 250 PHE 0.017 0.001 PHE M 394 TYR 0.022 0.001 TYR B 70 ARG 0.004 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7197 (t0) cc_final: 0.6884 (t0) REVERT: A 223 LYS cc_start: 0.6799 (ttpt) cc_final: 0.5861 (tptt) REVERT: B 83 MET cc_start: 0.7450 (ppp) cc_final: 0.6946 (ptm) REVERT: B 112 CYS cc_start: 0.8412 (t) cc_final: 0.7830 (m) REVERT: B 163 ASP cc_start: 0.7535 (p0) cc_final: 0.6967 (t0) REVERT: B 184 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7249 (mm) REVERT: M 98 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6926 (tm-30) REVERT: M 102 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8028 (mmtp) REVERT: M 108 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7946 (mp) REVERT: M 154 GLN cc_start: 0.7583 (pp30) cc_final: 0.7250 (pp30) REVERT: M 158 GLN cc_start: 0.7258 (tm-30) cc_final: 0.6338 (mt0) REVERT: M 410 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7837 (tptm) REVERT: S 139 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6865 (tm-30) outliers start: 21 outliers final: 16 residues processed: 188 average time/residue: 0.2859 time to fit residues: 77.0908 Evaluate side-chains 184 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 120 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 138 optimal weight: 0.0060 chunk 145 optimal weight: 5.9990 chunk 100 optimal weight: 0.0870 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS M 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14043 Z= 0.159 Angle : 0.490 7.199 19018 Z= 0.257 Chirality : 0.038 0.140 2215 Planarity : 0.003 0.036 2418 Dihedral : 4.104 52.174 1884 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 1.30 % Allowed : 12.91 % Favored : 85.79 % 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: 1.11 (0.20), residues: 1712 helix: 1.59 (0.16), residues: 995 sheet: 0.88 (0.39), residues: 168 loop : -0.87 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 462 HIS 0.003 0.001 HIS B 149 PHE 0.017 0.001 PHE M 394 TYR 0.020 0.001 TYR B 70 ARG 0.002 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7165 (t0) cc_final: 0.6877 (t0) REVERT: B 83 MET cc_start: 0.7466 (ppp) cc_final: 0.6872 (ptm) REVERT: B 99 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8691 (t0) REVERT: B 112 CYS cc_start: 0.8331 (t) cc_final: 0.7750 (m) REVERT: B 163 ASP cc_start: 0.7494 (p0) cc_final: 0.6962 (t0) REVERT: B 184 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7234 (mm) REVERT: M 185 MET cc_start: 0.6092 (tmm) cc_final: 0.4941 (tpp) REVERT: M 410 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7780 (tptm) outliers start: 20 outliers final: 15 residues processed: 188 average time/residue: 0.2664 time to fit residues: 73.1149 Evaluate side-chains 181 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 112 optimal weight: 0.8980 chunk 170 optimal weight: 0.0470 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14043 Z= 0.167 Angle : 0.499 7.101 19018 Z= 0.261 Chirality : 0.039 0.141 2215 Planarity : 0.003 0.039 2418 Dihedral : 4.065 50.962 1884 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 1.24 % Allowed : 13.30 % Favored : 85.46 % 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: 1.11 (0.20), residues: 1712 helix: 1.59 (0.16), residues: 990 sheet: 0.88 (0.39), residues: 168 loop : -0.84 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 462 HIS 0.003 0.001 HIS S 85 PHE 0.018 0.001 PHE M 394 TYR 0.021 0.001 TYR B 70 ARG 0.002 0.000 ARG B 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7135 (t0) cc_final: 0.6845 (t0) REVERT: B 99 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8717 (t0) REVERT: B 163 ASP cc_start: 0.7481 (p0) cc_final: 0.7062 (p0) REVERT: B 184 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7228 (mm) REVERT: M 185 MET cc_start: 0.6143 (tmm) cc_final: 0.4975 (tpp) REVERT: M 410 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7793 (tptm) REVERT: S 139 GLN cc_start: 0.7405 (tm-30) cc_final: 0.7085 (tm-30) outliers start: 19 outliers final: 12 residues processed: 181 average time/residue: 0.2770 time to fit residues: 73.2059 Evaluate side-chains 184 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS M 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.188503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146663 restraints weight = 16446.118| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.23 r_work: 0.3511 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1896 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: