Starting phenix.real_space_refine on Fri Feb 16 20:57:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4h_14312/02_2024/7r4h_14312_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4h_14312/02_2024/7r4h_14312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4h_14312/02_2024/7r4h_14312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4h_14312/02_2024/7r4h_14312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4h_14312/02_2024/7r4h_14312_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4h_14312/02_2024/7r4h_14312_updated.pdb" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 97 5.16 5 C 10476 2.51 5 N 2801 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "G ASP 236": "OD1" <-> "OD2" Residue "G ASP 260": "OD1" <-> "OD2" Residue "G GLU 265": "OE1" <-> "OE2" Residue "G GLU 291": "OE1" <-> "OE2" Residue "G ASP 358": "OD1" <-> "OD2" Residue "G PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 503": "OD1" <-> "OD2" Residue "G ASP 507": "OD1" <-> "OD2" Residue "H GLU 41": "OE1" <-> "OE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 164": "OD1" <-> "OD2" Residue "H GLU 168": "OE1" <-> "OE2" Residue "L GLU 362": "OE1" <-> "OE2" Residue "M GLU 93": "OE1" <-> "OE2" Residue "M GLU 100": "OE1" <-> "OE2" Residue "M GLU 337": "OE1" <-> "OE2" Residue "M ASP 369": "OD1" <-> "OD2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 75": "OD1" <-> "OD2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S ASP 137": "OD1" <-> "OD2" Residue "S ASP 139": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16485 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4513 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1330 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "G" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4633 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 13, 'TRANS': 571} Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "M" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3362 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "S" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1197 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.66, per 1000 atoms: 0.53 Number of scatterers: 16485 At special positions: 0 Unit cell: (122.4, 132.3, 130.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 97 16.00 P 7 15.00 Mg 2 11.99 O 3102 8.00 N 2801 7.00 C 10476 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 3.0 seconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 11 sheets defined 49.2% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'B' and resid 16 through 22 Processing helix chain 'B' and resid 27 through 42 Processing helix chain 'B' and resid 48 through 55 removed outlier: 3.537A pdb=" N PHE B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.508A pdb=" N VAL B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 55' Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 135 through 151 removed outlier: 3.734A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 174 through 190 Processing helix chain 'B' and resid 201 through 211 Processing helix chain 'B' and resid 216 through 228 removed outlier: 3.588A pdb=" N ILE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 249 Proline residue: B 246 - end of helix removed outlier: 4.878A pdb=" N SER B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 276 through 293 removed outlier: 3.900A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 4.082A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.776A pdb=" N GLN B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 312 " --> pdb=" O LEU B 308 " (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 344 removed outlier: 3.506A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.128A pdb=" N THR B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 385 through 399 removed outlier: 3.551A pdb=" N ALA B 388 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU B 389 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 393 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 4.572A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 462 through 475 removed outlier: 4.818A pdb=" N SER B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N PHE B 473 " --> pdb=" O PHE B 469 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N HIS B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 494 Processing helix chain 'B' and resid 500 through 511 removed outlier: 3.568A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 532 Processing helix chain 'B' and resid 534 through 541 removed outlier: 3.620A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 564 removed outlier: 3.678A pdb=" N GLU B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 97 through 110 removed outlier: 4.243A pdb=" N ASN C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 166 through 175 Processing helix chain 'G' and resid 7 through 15 Processing helix chain 'G' and resid 20 through 39 removed outlier: 3.684A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 59 Processing helix chain 'G' and resid 64 through 74 removed outlier: 3.911A pdb=" N GLN G 67 " --> pdb=" O HIS G 64 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU G 68 " --> pdb=" O PHE G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 100 through 111 removed outlier: 3.632A pdb=" N MET G 103 " --> pdb=" O HIS G 100 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 104 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN G 105 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE G 107 " --> pdb=" O THR G 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU G 111 " --> pdb=" O LYS G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 Processing helix chain 'G' and resid 134 through 137 No H-bonds generated for 'chain 'G' and resid 134 through 137' Processing helix chain 'G' and resid 139 through 145 removed outlier: 3.586A pdb=" N LEU G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 167 removed outlier: 3.895A pdb=" N LYS G 156 " --> pdb=" O TYR G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 188 through 204 Processing helix chain 'G' and resid 216 through 228 Processing helix chain 'G' and resid 243 through 255 Processing helix chain 'G' and resid 262 through 277 removed outlier: 4.597A pdb=" N ASP G 269 " --> pdb=" O GLU G 265 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE G 270 " --> pdb=" O ALA G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 298 Processing helix chain 'G' and resid 303 through 317 removed outlier: 3.570A pdb=" N VAL G 307 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 308 " --> pdb=" O GLY G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 334 Processing helix chain 'G' and resid 340 through 354 removed outlier: 3.753A pdb=" N GLN G 344 " --> pdb=" O HIS G 340 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG G 345 " --> pdb=" O ASN G 341 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS G 346 " --> pdb=" O ALA G 342 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG G 347 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER G 348 " --> pdb=" O GLN G 344 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR G 349 " --> pdb=" O ARG G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 371 Processing helix chain 'G' and resid 378 through 390 removed outlier: 4.067A pdb=" N GLU G 384 " --> pdb=" O GLY G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 410 Processing helix chain 'G' and resid 415 through 428 Processing helix chain 'G' and resid 430 through 432 No H-bonds generated for 'chain 'G' and resid 430 through 432' Processing helix chain 'G' and resid 438 through 447 Processing helix chain 'G' and resid 453 through 465 Processing helix chain 'G' and resid 470 through 487 removed outlier: 3.643A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU G 486 " --> pdb=" O GLU G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 514 Processing helix chain 'G' and resid 522 through 536 removed outlier: 4.259A pdb=" N THR G 535 " --> pdb=" O MET G 531 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG G 536 " --> pdb=" O LYS G 532 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 551 removed outlier: 3.866A pdb=" N TYR G 551 " --> pdb=" O VAL G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 572 Processing helix chain 'G' and resid 577 through 580 No H-bonds generated for 'chain 'G' and resid 577 through 580' Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 75 through 81 removed outlier: 3.604A pdb=" N TRP H 78 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS H 80 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 110 Processing helix chain 'H' and resid 136 through 143 Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 166 through 177 removed outlier: 3.818A pdb=" N LEU H 177 " --> pdb=" O LEU H 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 42 removed outlier: 4.277A pdb=" N MET M 34 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Proline residue: M 35 - end of helix removed outlier: 3.762A pdb=" N GLU M 42 " --> pdb=" O GLU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 94 Processing helix chain 'M' and resid 102 through 105 No H-bonds generated for 'chain 'M' and resid 102 through 105' Processing helix chain 'M' and resid 107 through 117 Processing helix chain 'M' and resid 128 through 131 No H-bonds generated for 'chain 'M' and resid 128 through 131' Processing helix chain 'M' and resid 151 through 153 No H-bonds generated for 'chain 'M' and resid 151 through 153' Processing helix chain 'M' and resid 217 through 223 Processing helix chain 'M' and resid 244 through 250 Processing helix chain 'S' and resid 25 through 40 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 129 through 141 Processing sheet with id= A, first strand: chain 'C' and resid 120 through 125 removed outlier: 7.282A pdb=" N ARG C 19 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ILE C 89 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU C 21 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL C 91 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C 23 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET C 18 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 64 " --> pdb=" O MET C 18 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 61 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 58 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 153 through 157 removed outlier: 6.479A pdb=" N LEU H 121 " --> pdb=" O TYR H 154 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLN H 156 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL H 123 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLY H 24 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 49 through 52 removed outlier: 3.769A pdb=" N ALA M 5 " --> pdb=" O THR M 70 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 381 through 383 Processing sheet with id= E, first strand: chain 'M' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'M' and resid 253 through 255 removed outlier: 4.234A pdb=" N ILE M 253 " --> pdb=" O LEU M 212 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR M 394 " --> pdb=" O GLY M 213 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 277 through 286 removed outlier: 3.666A pdb=" N ARG M 290 " --> pdb=" O HIS M 286 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE M 291 " --> pdb=" O PHE M 360 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= I, first strand: chain 'M' and resid 310 through 315 Processing sheet with id= J, first strand: chain 'M' and resid 198 through 202 removed outlier: 6.397A pdb=" N MET M 200 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU M 263 " --> pdb=" O MET M 200 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL M 202 " --> pdb=" O GLU M 261 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLU M 261 " --> pdb=" O VAL M 202 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 49 through 51 removed outlier: 3.812A pdb=" N PHE S 4 " --> pdb=" O ALA S 70 " (cutoff:3.500A) 734 hydrogen bonds defined for protein. 2079 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: 4.72 Time building geometry restraints manager: 7.08 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: 4636 1.34 - 1.46: 2967 1.46 - 1.58: 8983 1.58 - 1.70: 23 1.70 - 1.82: 158 Bond restraints: 16767 Sorted by residual: bond pdb=" CB ASN G 341 " pdb=" CG ASN G 341 " ideal model delta sigma weight residual 1.516 1.588 -0.072 2.50e-02 1.60e+03 8.41e+00 bond pdb=" C ARG C 75 " pdb=" N PRO C 76 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.22e+00 bond pdb=" CA ASN G 377 " pdb=" CB ASN G 377 " ideal model delta sigma weight residual 1.526 1.566 -0.040 1.68e-02 3.54e+03 5.74e+00 bond pdb=" CG1 ILE S 135 " pdb=" CD1 ILE S 135 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.42e+00 bond pdb=" CB GLN B 512 " pdb=" CG GLN B 512 " ideal model delta sigma weight residual 1.520 1.589 -0.069 3.00e-02 1.11e+03 5.34e+00 ... (remaining 16762 not shown) Histogram of bond angle deviations from ideal: 94.02 - 102.73: 85 102.73 - 111.45: 6648 111.45 - 120.16: 9096 120.16 - 128.88: 6735 128.88 - 137.59: 122 Bond angle restraints: 22686 Sorted by residual: angle pdb=" CB LYS B 26 " pdb=" CG LYS B 26 " pdb=" CD LYS B 26 " ideal model delta sigma weight residual 111.30 126.40 -15.10 2.30e+00 1.89e-01 4.31e+01 angle pdb=" CA LEU G 406 " pdb=" CB LEU G 406 " pdb=" CG LEU G 406 " ideal model delta sigma weight residual 116.30 137.59 -21.29 3.50e+00 8.16e-02 3.70e+01 angle pdb=" CA LYS G 546 " pdb=" CB LYS G 546 " pdb=" CG LYS G 546 " ideal model delta sigma weight residual 114.10 126.04 -11.94 2.00e+00 2.50e-01 3.56e+01 angle pdb=" CA GLU G 393 " pdb=" CB GLU G 393 " pdb=" CG GLU G 393 " ideal model delta sigma weight residual 114.10 126.01 -11.91 2.00e+00 2.50e-01 3.55e+01 angle pdb=" CA LYS G 383 " pdb=" CB LYS G 383 " pdb=" CG LYS G 383 " ideal model delta sigma weight residual 114.10 125.89 -11.79 2.00e+00 2.50e-01 3.48e+01 ... (remaining 22681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 9745 33.84 - 67.68: 502 67.68 - 101.52: 34 101.52 - 135.35: 3 135.35 - 169.19: 2 Dihedral angle restraints: 10286 sinusoidal: 4244 harmonic: 6042 Sorted by residual: dihedral pdb=" CA ASN C 175 " pdb=" C ASN C 175 " pdb=" N GLN C 176 " pdb=" CA GLN C 176 " ideal model delta harmonic sigma weight residual 180.00 143.91 36.09 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" C5' GTP H1001 " pdb=" O5' GTP H1001 " pdb=" PA GTP H1001 " pdb=" O3A GTP H1001 " ideal model delta sinusoidal sigma weight residual 69.27 -99.92 169.19 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP C1001 " pdb=" O5' GTP C1001 " pdb=" PA GTP C1001 " pdb=" O3A GTP C1001 " ideal model delta sinusoidal sigma weight residual 69.27 -132.85 -157.88 1 2.00e+01 2.50e-03 4.62e+01 ... (remaining 10283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2251 0.084 - 0.168: 323 0.168 - 0.251: 39 0.251 - 0.335: 5 0.335 - 0.419: 3 Chirality restraints: 2621 Sorted by residual: chirality pdb=" CG LEU G 256 " pdb=" CB LEU G 256 " pdb=" CD1 LEU G 256 " pdb=" CD2 LEU G 256 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CB VAL G 512 " pdb=" CA VAL G 512 " pdb=" CG1 VAL G 512 " pdb=" CG2 VAL G 512 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE G 550 " pdb=" CA ILE G 550 " pdb=" CG1 ILE G 550 " pdb=" CG2 ILE G 550 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 2618 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 104 " 0.358 9.50e-02 1.11e+02 1.61e-01 1.84e+01 pdb=" NE ARG C 104 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 104 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 104 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 104 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL M 316 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO M 317 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO M 317 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 317 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 46 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO C 47 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.039 5.00e-02 4.00e+02 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 353 2.67 - 3.23: 14175 3.23 - 3.79: 27818 3.79 - 4.34: 36956 4.34 - 4.90: 59734 Nonbonded interactions: 139036 Sorted by model distance: nonbonded pdb=" O2A GTP H1001 " pdb="MG MG H1002 " model vdw 2.119 2.170 nonbonded pdb=" O3A GTP C1001 " pdb="MG MG C1002 " model vdw 2.140 2.170 nonbonded pdb=" O3A GTP H1001 " pdb="MG MG H1002 " model vdw 2.160 2.170 nonbonded pdb=" O3G GTP C1001 " pdb="MG MG C1002 " model vdw 2.165 2.170 nonbonded pdb=" O VAL G 327 " pdb=" OG SER G 331 " model vdw 2.283 2.440 ... (remaining 139031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 17 through 179 or resid 1001 through 1002)) selection = chain 'H' } 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: 1.150 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: 0.020 Extract box with map and model: 6.470 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 45.370 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.006 0.091 16767 Z= 0.404 Angle : 1.223 21.290 22686 Z= 0.620 Chirality : 0.060 0.419 2621 Planarity : 0.009 0.161 2870 Dihedral : 19.220 169.193 6358 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.93 % Allowed : 33.01 % Favored : 63.06 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.15), residues: 2031 helix: -2.48 (0.11), residues: 1084 sheet: -1.06 (0.33), residues: 255 loop : -1.64 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 172 HIS 0.008 0.001 HIS G 340 PHE 0.018 0.003 PHE S 4 TYR 0.042 0.002 TYR H 58 ARG 0.027 0.001 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 185 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7534 (pm20) cc_final: 0.7322 (pm20) REVERT: G 265 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8542 (pp20) REVERT: G 450 GLU cc_start: 0.7726 (pm20) cc_final: 0.7467 (pm20) REVERT: M 303 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7454 (mtp85) REVERT: S 59 TYR cc_start: 0.8848 (p90) cc_final: 0.8630 (p90) outliers start: 72 outliers final: 56 residues processed: 249 average time/residue: 1.1880 time to fit residues: 332.8793 Evaluate side-chains 229 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 172 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 399 ASP Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 554 SER Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 128 SER Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain M residue 303 ARG Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 401 SER Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 48 SER Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 84 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS M 89 GLN M 288 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16767 Z= 0.204 Angle : 0.602 11.746 22686 Z= 0.303 Chirality : 0.042 0.171 2621 Planarity : 0.004 0.051 2870 Dihedral : 9.817 163.810 2342 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.41 % Allowed : 28.31 % Favored : 66.28 % 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: -1.42 (0.17), residues: 2031 helix: -0.73 (0.14), residues: 1099 sheet: -0.69 (0.31), residues: 269 loop : -1.08 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 172 HIS 0.005 0.001 HIS S 3 PHE 0.018 0.001 PHE S 67 TYR 0.024 0.001 TYR H 58 ARG 0.006 0.000 ARG M 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 174 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.7706 (tptp) cc_final: 0.7313 (tptp) REVERT: B 175 MET cc_start: 0.8152 (mpt) cc_final: 0.7941 (mpt) REVERT: B 397 ASP cc_start: 0.8379 (m-30) cc_final: 0.8090 (m-30) REVERT: B 469 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6356 (t80) REVERT: C 55 THR cc_start: 0.8862 (m) cc_final: 0.8575 (t) REVERT: C 108 MET cc_start: 0.7028 (mmt) cc_final: 0.6704 (mmm) REVERT: C 134 MET cc_start: 0.2680 (pmt) cc_final: 0.2239 (pmm) REVERT: G 376 ASN cc_start: 0.8258 (m-40) cc_final: 0.7586 (p0) REVERT: G 450 GLU cc_start: 0.7630 (pm20) cc_final: 0.7341 (pm20) REVERT: H 105 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7589 (mm-30) REVERT: L 359 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: L 365 ILE cc_start: 0.7449 (pp) cc_final: 0.7182 (mt) REVERT: M 225 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7654 (ptt180) outliers start: 99 outliers final: 46 residues processed: 255 average time/residue: 1.2364 time to fit residues: 352.9910 Evaluate side-chains 212 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 163 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 399 ASP Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 584 MET Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 24 ASP Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 225 ARG Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 198 optimal weight: 0.4980 chunk 163 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN G 97 GLN G 112 ASN G 218 GLN G 340 HIS ** G 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN S 3 HIS S 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 16767 Z= 0.367 Angle : 0.673 16.036 22686 Z= 0.334 Chirality : 0.046 0.151 2621 Planarity : 0.004 0.048 2870 Dihedral : 9.670 163.411 2296 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 6.78 % Allowed : 25.90 % Favored : 67.32 % 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: -0.59 (0.18), residues: 2031 helix: 0.08 (0.15), residues: 1085 sheet: -0.64 (0.30), residues: 276 loop : -0.82 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 172 HIS 0.011 0.001 HIS S 3 PHE 0.016 0.002 PHE G 117 TYR 0.020 0.002 TYR G 290 ARG 0.007 0.001 ARG M 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 177 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.7911 (tptp) cc_final: 0.7406 (tptp) REVERT: B 122 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8073 (pp) REVERT: B 269 MET cc_start: 0.8039 (tpp) cc_final: 0.7825 (mmm) REVERT: B 397 ASP cc_start: 0.8462 (m-30) cc_final: 0.8193 (m-30) REVERT: B 460 ASP cc_start: 0.7770 (m-30) cc_final: 0.7242 (p0) REVERT: B 469 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7174 (t80) REVERT: C 55 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8706 (t) REVERT: C 108 MET cc_start: 0.7220 (mmt) cc_final: 0.6908 (mmm) REVERT: G 450 GLU cc_start: 0.7615 (pm20) cc_final: 0.7300 (pm20) REVERT: G 546 LYS cc_start: 0.8039 (pptt) cc_final: 0.7703 (pptt) REVERT: H 58 TYR cc_start: 0.8571 (t80) cc_final: 0.8333 (t80) REVERT: H 83 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8529 (mt0) REVERT: H 104 ARG cc_start: 0.7933 (ttt90) cc_final: 0.7484 (ttp-110) REVERT: H 105 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7436 (mm-30) REVERT: L 359 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: L 365 ILE cc_start: 0.7393 (pp) cc_final: 0.7179 (mt) REVERT: M 130 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8531 (pp) REVERT: M 177 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: S 10 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.8029 (mtt90) REVERT: S 26 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8796 (mppt) outliers start: 124 outliers final: 56 residues processed: 279 average time/residue: 1.2276 time to fit residues: 383.5008 Evaluate side-chains 223 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 160 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 164 ILE Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 26 LYS Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 chunk 174 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 176 GLN G 283 ASN G 340 HIS G 447 ASN G 542 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16767 Z= 0.179 Angle : 0.577 14.470 22686 Z= 0.284 Chirality : 0.042 0.206 2621 Planarity : 0.004 0.045 2870 Dihedral : 9.241 160.193 2288 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.14 % Allowed : 27.54 % Favored : 67.32 % 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: -0.16 (0.18), residues: 2031 helix: 0.52 (0.16), residues: 1077 sheet: -0.60 (0.31), residues: 276 loop : -0.71 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 172 HIS 0.004 0.001 HIS G 235 PHE 0.012 0.001 PHE G 117 TYR 0.016 0.001 TYR G 387 ARG 0.004 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 165 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8003 (tptp) cc_final: 0.7481 (tptp) REVERT: B 122 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7982 (pp) REVERT: B 175 MET cc_start: 0.8384 (mpt) cc_final: 0.8182 (mpt) REVERT: B 397 ASP cc_start: 0.8450 (m-30) cc_final: 0.8167 (m-30) REVERT: B 460 ASP cc_start: 0.7717 (m-30) cc_final: 0.7213 (p0) REVERT: B 469 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7124 (t80) REVERT: C 108 MET cc_start: 0.7336 (mmt) cc_final: 0.7021 (mmm) REVERT: G 56 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8253 (mtt) REVERT: G 300 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8122 (ptmm) REVERT: G 450 GLU cc_start: 0.7596 (pm20) cc_final: 0.7257 (pm20) REVERT: G 546 LYS cc_start: 0.7999 (pptt) cc_final: 0.7622 (pptt) REVERT: H 83 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8460 (mt0) REVERT: H 104 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7477 (ttp-110) REVERT: H 105 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7493 (mm-30) REVERT: L 359 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: M 130 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8495 (pp) REVERT: M 209 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7522 (tp30) REVERT: M 285 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8290 (tptp) REVERT: S 25 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7962 (t0) REVERT: S 26 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8788 (mppt) REVERT: S 45 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7611 (pmm150) outliers start: 94 outliers final: 44 residues processed: 242 average time/residue: 1.3125 time to fit residues: 354.3358 Evaluate side-chains 207 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 152 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 399 ASP Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 285 LYS Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 26 LYS Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 0.0870 chunk 110 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 145 optimal weight: 0.4980 chunk 80 optimal weight: 0.0370 chunk 166 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN G 340 HIS G 542 ASN H 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16767 Z= 0.146 Angle : 0.542 14.220 22686 Z= 0.267 Chirality : 0.041 0.161 2621 Planarity : 0.003 0.043 2870 Dihedral : 8.876 161.180 2282 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.48 % Allowed : 27.60 % Favored : 67.92 % 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: 0.13 (0.19), residues: 2031 helix: 0.77 (0.16), residues: 1078 sheet: -0.48 (0.31), residues: 275 loop : -0.59 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 172 HIS 0.004 0.000 HIS G 235 PHE 0.010 0.001 PHE G 117 TYR 0.023 0.001 TYR H 58 ARG 0.006 0.000 ARG M 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 164 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8112 (tptp) cc_final: 0.7615 (tptp) REVERT: B 60 THR cc_start: 0.8637 (p) cc_final: 0.8275 (t) REVERT: B 189 GLU cc_start: 0.7519 (pt0) cc_final: 0.7183 (tm-30) REVERT: B 397 ASP cc_start: 0.8379 (m-30) cc_final: 0.8117 (m-30) REVERT: B 439 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4898 (pp) REVERT: B 460 ASP cc_start: 0.7668 (m-30) cc_final: 0.7173 (p0) REVERT: B 469 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7068 (t80) REVERT: C 108 MET cc_start: 0.7518 (mmt) cc_final: 0.7220 (mmm) REVERT: G 56 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8137 (mtt) REVERT: G 546 LYS cc_start: 0.7994 (pptt) cc_final: 0.7664 (pptt) REVERT: H 83 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8411 (mt0) REVERT: H 104 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7418 (ttp-110) REVERT: H 105 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7232 (mm-30) REVERT: L 359 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: S 25 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7956 (t0) REVERT: S 26 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8839 (mppt) outliers start: 82 outliers final: 37 residues processed: 228 average time/residue: 1.3054 time to fit residues: 330.9856 Evaluate side-chains 194 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 26 LYS Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN C 176 GLN ** G 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 HIS G 447 ASN H 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16767 Z= 0.180 Angle : 0.553 13.255 22686 Z= 0.271 Chirality : 0.042 0.180 2621 Planarity : 0.003 0.043 2870 Dihedral : 8.836 160.313 2276 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.48 % Allowed : 28.20 % Favored : 67.32 % 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: 0.29 (0.19), residues: 2031 helix: 0.91 (0.16), residues: 1075 sheet: -0.44 (0.31), residues: 275 loop : -0.52 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 172 HIS 0.003 0.001 HIS G 235 PHE 0.010 0.001 PHE G 117 TYR 0.027 0.001 TYR H 58 ARG 0.007 0.000 ARG M 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 159 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8159 (tptp) cc_final: 0.7779 (tptp) REVERT: B 60 THR cc_start: 0.8657 (p) cc_final: 0.8308 (t) REVERT: B 189 GLU cc_start: 0.7509 (pt0) cc_final: 0.7154 (tm-30) REVERT: B 439 LEU cc_start: 0.5216 (OUTLIER) cc_final: 0.4883 (pp) REVERT: B 460 ASP cc_start: 0.7699 (m-30) cc_final: 0.7213 (p0) REVERT: B 469 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7032 (t80) REVERT: C 108 MET cc_start: 0.7514 (mmt) cc_final: 0.7228 (mmm) REVERT: G 56 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8237 (mtt) REVERT: G 546 LYS cc_start: 0.7998 (pptt) cc_final: 0.7661 (pptt) REVERT: H 83 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8408 (mt0) REVERT: H 104 ARG cc_start: 0.7927 (ttt90) cc_final: 0.7431 (ttp-110) REVERT: H 105 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7238 (mm-30) REVERT: H 130 LEU cc_start: 0.7271 (pt) cc_final: 0.7042 (pp) REVERT: L 359 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: M 130 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8444 (pp) REVERT: M 177 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: S 25 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8012 (t0) REVERT: S 26 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8839 (mppt) REVERT: S 45 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7564 (pmm150) outliers start: 82 outliers final: 44 residues processed: 224 average time/residue: 1.3768 time to fit residues: 345.3379 Evaluate side-chains 207 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 154 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 399 ASP Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 26 LYS Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN G 97 GLN ** G 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 HIS G 447 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16767 Z= 0.212 Angle : 0.575 12.912 22686 Z= 0.281 Chirality : 0.042 0.199 2621 Planarity : 0.004 0.043 2870 Dihedral : 8.899 159.791 2276 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.75 % Allowed : 27.60 % Favored : 67.65 % 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: 0.33 (0.19), residues: 2031 helix: 0.93 (0.16), residues: 1079 sheet: -0.45 (0.30), residues: 274 loop : -0.47 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 172 HIS 0.003 0.001 HIS M 239 PHE 0.011 0.001 PHE G 117 TYR 0.026 0.001 TYR H 58 ARG 0.008 0.000 ARG M 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 157 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8206 (tptp) cc_final: 0.7889 (tptp) REVERT: B 60 THR cc_start: 0.8639 (p) cc_final: 0.8283 (t) REVERT: B 189 GLU cc_start: 0.7510 (pt0) cc_final: 0.7194 (tm-30) REVERT: B 397 ASP cc_start: 0.8394 (m-30) cc_final: 0.8160 (m-30) REVERT: B 439 LEU cc_start: 0.5360 (OUTLIER) cc_final: 0.5063 (pp) REVERT: B 460 ASP cc_start: 0.7783 (m-30) cc_final: 0.7338 (p0) REVERT: B 469 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7321 (t80) REVERT: C 108 MET cc_start: 0.7544 (mmt) cc_final: 0.7257 (mmm) REVERT: G 56 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8342 (mtt) REVERT: G 546 LYS cc_start: 0.7992 (pptt) cc_final: 0.7546 (pptt) REVERT: H 83 GLN cc_start: 0.8793 (mt0) cc_final: 0.8493 (mt0) REVERT: H 104 ARG cc_start: 0.7935 (ttt90) cc_final: 0.7428 (ttp-110) REVERT: H 105 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7478 (mm-30) REVERT: H 130 LEU cc_start: 0.7310 (pt) cc_final: 0.7044 (pp) REVERT: L 359 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6493 (tm-30) REVERT: M 130 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8455 (pp) REVERT: M 168 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8637 (ttmt) REVERT: M 177 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: M 209 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: M 337 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8802 (mp0) REVERT: S 25 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8042 (t0) REVERT: S 26 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8866 (mppt) REVERT: S 45 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7570 (pmm150) outliers start: 87 outliers final: 49 residues processed: 228 average time/residue: 1.2903 time to fit residues: 328.0396 Evaluate side-chains 212 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 151 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 584 MET Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 152 THR Chi-restraints excluded: chain M residue 164 ILE Chi-restraints excluded: chain M residue 168 LYS Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 26 LYS Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 0.0070 chunk 153 optimal weight: 3.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN G 97 GLN ** G 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 HIS G 447 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16767 Z= 0.169 Angle : 0.559 12.659 22686 Z= 0.273 Chirality : 0.042 0.208 2621 Planarity : 0.003 0.043 2870 Dihedral : 8.796 160.581 2276 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.88 % Allowed : 28.42 % Favored : 67.70 % 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: 0.40 (0.19), residues: 2031 helix: 0.99 (0.16), residues: 1075 sheet: -0.47 (0.31), residues: 273 loop : -0.42 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 172 HIS 0.003 0.001 HIS G 235 PHE 0.009 0.001 PHE G 117 TYR 0.025 0.001 TYR H 58 ARG 0.008 0.000 ARG M 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 155 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8202 (tptp) cc_final: 0.7890 (tptp) REVERT: B 60 THR cc_start: 0.8657 (p) cc_final: 0.8308 (t) REVERT: B 189 GLU cc_start: 0.7448 (pt0) cc_final: 0.7143 (tm-30) REVERT: B 397 ASP cc_start: 0.8411 (m-30) cc_final: 0.8172 (m-30) REVERT: B 439 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.4939 (pp) REVERT: B 460 ASP cc_start: 0.7756 (m-30) cc_final: 0.7340 (p0) REVERT: B 469 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7347 (t80) REVERT: B 498 GLU cc_start: 0.8389 (pm20) cc_final: 0.8119 (pm20) REVERT: C 108 MET cc_start: 0.7604 (mmt) cc_final: 0.7312 (mmm) REVERT: G 340 HIS cc_start: 0.7474 (t70) cc_final: 0.7266 (t-90) REVERT: G 379 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8329 (mtp85) REVERT: G 381 MET cc_start: 0.7162 (mpt) cc_final: 0.6834 (mpt) REVERT: G 546 LYS cc_start: 0.7970 (pptt) cc_final: 0.7541 (pptt) REVERT: H 83 GLN cc_start: 0.8777 (mt0) cc_final: 0.8475 (mt0) REVERT: L 359 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: M 177 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: M 209 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: M 337 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8810 (mp0) REVERT: M 399 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: S 25 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8005 (t0) REVERT: S 26 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8851 (mppt) REVERT: S 45 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7558 (pmm150) outliers start: 71 outliers final: 44 residues processed: 213 average time/residue: 1.3826 time to fit residues: 325.8589 Evaluate side-chains 204 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 149 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 ASP Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 399 GLU Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 26 LYS Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 3.9990 chunk 186 optimal weight: 0.0870 chunk 170 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 163 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 180 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN M 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16767 Z= 0.166 Angle : 0.557 12.723 22686 Z= 0.272 Chirality : 0.041 0.164 2621 Planarity : 0.003 0.042 2870 Dihedral : 8.735 160.592 2276 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.61 % Allowed : 28.96 % Favored : 67.43 % 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: 0.47 (0.19), residues: 2031 helix: 1.06 (0.16), residues: 1071 sheet: -0.45 (0.31), residues: 273 loop : -0.40 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 172 HIS 0.004 0.001 HIS G 235 PHE 0.009 0.001 PHE G 117 TYR 0.027 0.001 TYR H 58 ARG 0.009 0.000 ARG M 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 154 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8205 (tptp) cc_final: 0.7939 (tptp) REVERT: B 60 THR cc_start: 0.8653 (p) cc_final: 0.8305 (t) REVERT: B 460 ASP cc_start: 0.7759 (m-30) cc_final: 0.7339 (p0) REVERT: B 498 GLU cc_start: 0.8377 (pm20) cc_final: 0.8115 (pm20) REVERT: C 108 MET cc_start: 0.7621 (mmt) cc_final: 0.7334 (mmm) REVERT: G 300 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8165 (ptmm) REVERT: G 357 LEU cc_start: 0.8412 (mm) cc_final: 0.8108 (tm) REVERT: G 379 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8266 (mtp85) REVERT: G 546 LYS cc_start: 0.7969 (pptt) cc_final: 0.7532 (pptt) REVERT: H 83 GLN cc_start: 0.8739 (mt0) cc_final: 0.8456 (mt0) REVERT: L 359 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: M 177 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: M 209 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: M 337 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8820 (mp0) REVERT: M 399 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.6314 (tm-30) REVERT: S 25 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8023 (t0) REVERT: S 45 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7542 (pmm150) outliers start: 66 outliers final: 46 residues processed: 212 average time/residue: 1.3380 time to fit residues: 316.5711 Evaluate side-chains 204 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 149 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 399 GLU Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 0.5980 chunk 191 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 91 optimal weight: 0.0870 chunk 133 optimal weight: 0.0270 chunk 201 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 160 optimal weight: 0.0270 chunk 16 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN G 97 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16767 Z= 0.137 Angle : 0.544 12.954 22686 Z= 0.264 Chirality : 0.041 0.173 2621 Planarity : 0.003 0.042 2870 Dihedral : 8.559 162.309 2276 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.95 % Allowed : 29.45 % Favored : 67.60 % 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: 0.55 (0.19), residues: 2031 helix: 1.15 (0.16), residues: 1072 sheet: -0.35 (0.31), residues: 267 loop : -0.45 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 172 HIS 0.004 0.000 HIS G 100 PHE 0.008 0.001 PHE S 67 TYR 0.025 0.001 TYR H 58 ARG 0.009 0.000 ARG M 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 160 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8176 (tptp) cc_final: 0.7837 (tptp) REVERT: B 60 THR cc_start: 0.8612 (p) cc_final: 0.8267 (t) REVERT: B 460 ASP cc_start: 0.7751 (m-30) cc_final: 0.7319 (p0) REVERT: B 469 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7335 (t80) REVERT: C 108 MET cc_start: 0.7596 (mmt) cc_final: 0.7303 (mmm) REVERT: G 357 LEU cc_start: 0.8363 (mm) cc_final: 0.8080 (tm) REVERT: G 379 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8235 (mtp85) REVERT: G 546 LYS cc_start: 0.7953 (pptt) cc_final: 0.7562 (pptt) REVERT: H 83 GLN cc_start: 0.8739 (mt0) cc_final: 0.8355 (mt0) REVERT: L 359 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: M 177 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: M 337 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8796 (mp0) REVERT: M 399 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: S 45 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7492 (pmm150) REVERT: S 139 ASP cc_start: 0.8176 (m-30) cc_final: 0.7975 (m-30) outliers start: 54 outliers final: 41 residues processed: 205 average time/residue: 1.3414 time to fit residues: 306.0188 Evaluate side-chains 200 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 152 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 399 GLU Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 0.9990 chunk 170 optimal weight: 0.0020 chunk 49 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN C 176 GLN G 20 GLN G 97 GLN ** G 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.107892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075473 restraints weight = 28840.819| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.43 r_work: 0.3020 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16767 Z= 0.200 Angle : 0.570 12.585 22686 Z= 0.278 Chirality : 0.042 0.174 2621 Planarity : 0.003 0.042 2870 Dihedral : 8.672 160.400 2275 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.28 % Allowed : 29.56 % Favored : 67.16 % 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: 0.57 (0.19), residues: 2031 helix: 1.14 (0.16), residues: 1072 sheet: -0.40 (0.31), residues: 273 loop : -0.36 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 172 HIS 0.004 0.001 HIS G 100 PHE 0.010 0.001 PHE G 117 TYR 0.024 0.001 TYR H 58 ARG 0.009 0.000 ARG M 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6686.08 seconds wall clock time: 119 minutes 30.27 seconds (7170.27 seconds total)