Starting phenix.real_space_refine on Sun Dec 10 07:44:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/12_2023/8t1o_40973_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/12_2023/8t1o_40973.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/12_2023/8t1o_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_40973/12_2023/8t1o_40973_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/12_2023/8t1o_40973_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/12_2023/8t1o_40973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/12_2023/8t1o_40973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/12_2023/8t1o_40973_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1o_40973/12_2023/8t1o_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-1.21rc1-5172/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: 7.41, 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: 6.26 Conformation dependent library (CDL) restraints added in 2.6 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: 3.00 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: 3.95 Time building geometry restraints manager: 6.11 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: 2.570 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: 12.690 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 39.370 Find NCS groups from input model: 0.440 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.320 ------------------------------------------------------------------------------- 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 : 1.683 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2857 time to fit residues: 88.3422 Evaluate side-chains 177 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3293 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.6607 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14043 Z= 0.166 Angle : 0.514 7.431 19018 Z= 0.271 Chirality : 0.039 0.146 2215 Planarity : 0.004 0.036 2418 Dihedral : 4.501 57.686 1884 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 0.65 % Allowed : 6.84 % Favored : 92.50 % 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: 1.40 (0.16), residues: 995 sheet: 0.83 (0.38), residues: 166 loop : -0.76 (0.26), residues: 551 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 198 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 1.691 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 192 average time/residue: 0.2756 time to fit residues: 77.2148 Evaluate side-chains 183 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 177 time to evaluate : 1.699 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1309 time to fit residues: 3.7923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 105 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.6642 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14043 Z= 0.214 Angle : 0.519 6.451 19018 Z= 0.273 Chirality : 0.040 0.180 2215 Planarity : 0.004 0.037 2418 Dihedral : 4.461 59.209 1884 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.52 % Allowed : 9.45 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1712 helix: 1.34 (0.16), residues: 993 sheet: 0.75 (0.39), residues: 162 loop : -0.83 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 462 HIS 0.004 0.001 HIS A 320 PHE 0.011 0.001 PHE S 4 TYR 0.017 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 194 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 1.722 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 193 average time/residue: 0.2810 time to fit residues: 79.2193 Evaluate side-chains 177 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1332 time to fit residues: 3.0424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 chunk 44 optimal weight: 0.0020 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 318 GLN S 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14043 Z= 0.169 Angle : 0.489 6.482 19018 Z= 0.256 Chirality : 0.039 0.142 2215 Planarity : 0.003 0.036 2418 Dihedral : 4.341 59.254 1884 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 0.65 % Allowed : 10.23 % Favored : 89.11 % 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: 0.93 (0.20), residues: 1712 helix: 1.43 (0.16), residues: 993 sheet: 0.74 (0.39), residues: 166 loop : -0.86 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 462 HIS 0.004 0.001 HIS M 10 PHE 0.010 0.001 PHE M 81 TYR 0.018 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 202 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 1.949 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 197 average time/residue: 0.2820 time to fit residues: 80.0820 Evaluate side-chains 182 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1227 time to fit residues: 3.3976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 2 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 0.0170 chunk 148 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN M 154 GLN M 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14043 Z= 0.206 Angle : 0.506 6.527 19018 Z= 0.265 Chirality : 0.040 0.145 2215 Planarity : 0.003 0.036 2418 Dihedral : 4.318 57.860 1884 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.04 % Allowed : 10.95 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1712 helix: 1.37 (0.16), residues: 998 sheet: 0.82 (0.39), residues: 166 loop : -0.88 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 462 HIS 0.004 0.001 HIS B 250 PHE 0.012 0.001 PHE S 4 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 195 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.660 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 188 average time/residue: 0.2780 time to fit residues: 76.3352 Evaluate side-chains 183 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 1.751 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1375 time to fit residues: 4.0291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.3980 chunk 148 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 165 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** M 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14043 Z= 0.198 Angle : 0.515 8.551 19018 Z= 0.268 Chirality : 0.039 0.142 2215 Planarity : 0.003 0.036 2418 Dihedral : 4.277 56.571 1884 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 0.59 % Allowed : 12.26 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1712 helix: 1.37 (0.16), residues: 999 sheet: 0.81 (0.40), residues: 165 loop : -0.87 (0.26), residues: 548 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 0.011 0.001 PHE S 4 TYR 0.021 0.001 TYR B 70 ARG 0.002 0.000 ARG S 42 *********************** 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 189 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 1.598 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 186 average time/residue: 0.2756 time to fit residues: 74.3331 Evaluate side-chains 174 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 1.726 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1425 time to fit residues: 3.9001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 164 optimal weight: 0.0870 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 41 GLN M 100 ASN M 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14043 Z= 0.201 Angle : 0.511 6.239 19018 Z= 0.269 Chirality : 0.039 0.146 2215 Planarity : 0.003 0.036 2418 Dihedral : 4.259 55.208 1884 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 0.52 % Allowed : 12.71 % Favored : 86.77 % 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: 0.87 (0.20), residues: 1712 helix: 1.35 (0.16), residues: 996 sheet: 0.82 (0.40), residues: 165 loop : -0.87 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 462 HIS 0.004 0.001 HIS B 149 PHE 0.016 0.001 PHE M 394 TYR 0.020 0.001 TYR B 70 ARG 0.002 0.000 ARG M 21 *********************** 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 182 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 1.827 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 176 average time/residue: 0.3006 time to fit residues: 76.5413 Evaluate side-chains 165 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1530 time to fit residues: 3.2746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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: 0.6665 moved from start: 0.1796 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= 0.221 Angle : 0.536 9.770 19018 Z= 0.278 Chirality : 0.040 0.146 2215 Planarity : 0.004 0.037 2418 Dihedral : 4.239 53.839 1884 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 0.26 % Allowed : 13.75 % 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: 0.86 (0.20), residues: 1712 helix: 1.34 (0.16), residues: 995 sheet: 0.87 (0.40), residues: 165 loop : -0.88 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.004 0.001 HIS B 149 PHE 0.016 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 172 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 169 average time/residue: 0.2991 time to fit residues: 72.9074 Evaluate side-chains 170 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.644 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1378 time to fit residues: 2.5691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 153 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 0.0020 chunk 120 optimal weight: 0.0000 chunk 47 optimal weight: 0.9980 chunk 138 optimal weight: 0.0070 chunk 145 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.3610 ------------------------------------------------------------------------------- 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: 0.6629 moved from start: 0.1863 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 : 0.507 6.994 19018 Z= 0.266 Chirality : 0.039 0.150 2215 Planarity : 0.003 0.036 2418 Dihedral : 4.152 52.605 1884 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 0.07 % Allowed : 14.34 % Favored : 85.59 % 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: 0.99 (0.20), residues: 1712 helix: 1.48 (0.16), residues: 995 sheet: 0.90 (0.39), residues: 165 loop : -0.91 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 462 HIS 0.004 0.001 HIS B 149 PHE 0.016 0.001 PHE M 394 TYR 0.022 0.001 TYR B 121 ARG 0.002 0.000 ARG S 42 *********************** 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 178 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.708 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.2865 time to fit residues: 74.1023 Evaluate side-chains 170 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.623 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1675 time to fit residues: 2.5658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 0.0060 chunk 112 optimal weight: 0.9980 chunk 170 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 83 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 M 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14043 Z= 0.170 Angle : 0.518 10.767 19018 Z= 0.269 Chirality : 0.039 0.137 2215 Planarity : 0.003 0.037 2418 Dihedral : 4.100 51.169 1884 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 0.20 % Allowed : 14.54 % Favored : 85.27 % 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: 1.51 (0.16), residues: 995 sheet: 0.87 (0.39), residues: 166 loop : -0.88 (0.26), residues: 551 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 0.019 0.001 PHE M 394 TYR 0.022 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 177 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 1.724 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 176 average time/residue: 0.2986 time to fit residues: 76.8072 Evaluate side-chains 169 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1565 time to fit residues: 2.8296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 M 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.188769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146305 restraints weight = 16608.840| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.35 r_work: 0.3487 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14043 Z= 0.276 Angle : 0.561 10.349 19018 Z= 0.292 Chirality : 0.041 0.154 2215 Planarity : 0.004 0.037 2418 Dihedral : 4.242 49.506 1884 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 0.13 % Allowed : 14.86 % Favored : 85.01 % 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: 0.78 (0.20), residues: 1712 helix: 1.25 (0.16), residues: 992 sheet: 0.71 (0.39), residues: 173 loop : -0.82 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.005 0.001 HIS A 302 PHE 0.018 0.001 PHE M 394 TYR 0.024 0.002 TYR B 70 ARG 0.003 0.000 ARG M 427 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3058.90 seconds wall clock time: 57 minutes 52.83 seconds (3472.83 seconds total)