Starting phenix.real_space_refine on Fri Mar 15 18:44:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fe8_4241/03_2024/6fe8_4241.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fe8_4241/03_2024/6fe8_4241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fe8_4241/03_2024/6fe8_4241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fe8_4241/03_2024/6fe8_4241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fe8_4241/03_2024/6fe8_4241.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fe8_4241/03_2024/6fe8_4241.pdb" } resolution = 3.7 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 8120 2.51 5 N 2055 2.21 5 O 2249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D ARG 463": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12479 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4320 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 4249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4249 Classifications: {'peptide': 512} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 495} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1137 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2773 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain breaks: 3 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 10, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 175 Time building chain proxies: 6.85, per 1000 atoms: 0.55 Number of scatterers: 12479 At special positions: 0 Unit cell: (103.88, 117.66, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2249 8.00 N 2055 7.00 C 8120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 215 " distance=2.04 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 215 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.4 seconds 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 7 sheets defined 64.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.778A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.818A pdb=" N TYR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.855A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 147 removed outlier: 4.045A pdb=" N ARG A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 173 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.684A pdb=" N HIS A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.685A pdb=" N GLY A 203 " --> pdb=" O TRP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 222 Processing helix chain 'A' and resid 230 through 241 removed outlier: 4.484A pdb=" N VAL A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.518A pdb=" N PHE A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.837A pdb=" N HIS A 456 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 477 removed outlier: 3.870A pdb=" N ILE A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.894A pdb=" N LYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 524 removed outlier: 3.795A pdb=" N LEU A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 551 removed outlier: 3.536A pdb=" N LYS A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 Processing helix chain 'A' and resid 589 through 601 Processing helix chain 'A' and resid 602 through 607 removed outlier: 3.609A pdb=" N ASP A 605 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 72 removed outlier: 4.461A pdb=" N ASP B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.576A pdb=" N TYR B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 removed outlier: 3.821A pdb=" N PHE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.665A pdb=" N TYR B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 153 through 173 removed outlier: 3.520A pdb=" N TYR B 173 " --> pdb=" O MET B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.579A pdb=" N HIS B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.572A pdb=" N LEU B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.687A pdb=" N GLU B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 266 Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 393 through 421 removed outlier: 3.798A pdb=" N ARG B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.572A pdb=" N PHE B 453 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.902A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 495 removed outlier: 3.629A pdb=" N ALA B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 524 Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.730A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 563 Processing helix chain 'B' and resid 589 through 601 Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.616A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 28 through 33 Processing helix chain 'C' and resid 83 through 97 Processing helix chain 'C' and resid 107 through 113 removed outlier: 3.709A pdb=" N LYS C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 Processing helix chain 'C' and resid 127 through 141 Processing helix chain 'C' and resid 143 through 160 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.662A pdb=" N GLU D 11 " --> pdb=" O VAL D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 removed outlier: 3.893A pdb=" N HIS D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 111 removed outlier: 3.622A pdb=" N LEU D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 Processing helix chain 'D' and resid 176 through 190 removed outlier: 4.071A pdb=" N LYS D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 removed outlier: 3.757A pdb=" N SER D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 288 removed outlier: 3.902A pdb=" N TYR D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 381 removed outlier: 3.645A pdb=" N LYS D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 Processing helix chain 'D' and resid 419 through 432 Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 removed outlier: 4.007A pdb=" N TYR A 534 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA4, first strand: chain 'C' and resid 15 through 19 removed outlier: 8.685A pdb=" N MET C 77 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 7 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 118 through 123 removed outlier: 6.517A pdb=" N LEU D 129 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TRP D 141 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR D 131 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 198 through 200 removed outlier: 6.616A pdb=" N VAL D 199 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE D 276 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE D 312 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU D 337 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE D 440 " --> pdb=" O GLU D 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 391 through 392 removed outlier: 6.096A pdb=" N ARG D 409 " --> pdb=" O VAL D 475 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL D 477 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS D 411 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE D 452 " --> pdb=" O GLN D 474 " (cutoff:3.500A) 669 hydrogen bonds defined for protein. 1971 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 5.44 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: 3865 1.34 - 1.46: 2375 1.46 - 1.58: 6437 1.58 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 12766 Sorted by residual: bond pdb=" C LEU A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.60e+00 bond pdb=" C TYR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.25e-02 6.40e+03 2.52e+00 bond pdb=" CB ASN A 394 " pdb=" CG ASN A 394 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.52e+00 bond pdb=" CA LEU A 302 " pdb=" C LEU A 302 " ideal model delta sigma weight residual 1.518 1.580 -0.062 4.01e-02 6.22e+02 2.40e+00 bond pdb=" CA ASN A 394 " pdb=" CB ASN A 394 " ideal model delta sigma weight residual 1.533 1.558 -0.025 1.66e-02 3.63e+03 2.27e+00 ... (remaining 12761 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.43: 189 105.43 - 112.63: 6529 112.63 - 119.83: 4531 119.83 - 127.03: 5918 127.03 - 134.22: 148 Bond angle restraints: 17315 Sorted by residual: angle pdb=" N ASN D 451 " pdb=" CA ASN D 451 " pdb=" C ASN D 451 " ideal model delta sigma weight residual 110.91 116.55 -5.64 1.17e+00 7.31e-01 2.33e+01 angle pdb=" C VAL D 445 " pdb=" N SER D 446 " pdb=" CA SER D 446 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C SER A 393 " pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 123.91 130.52 -6.61 1.66e+00 3.63e-01 1.59e+01 angle pdb=" CA LEU D 12 " pdb=" CB LEU D 12 " pdb=" CG LEU D 12 " ideal model delta sigma weight residual 116.30 129.99 -13.69 3.50e+00 8.16e-02 1.53e+01 angle pdb=" N TYR A 335 " pdb=" CA TYR A 335 " pdb=" C TYR A 335 " ideal model delta sigma weight residual 114.64 108.81 5.83 1.52e+00 4.33e-01 1.47e+01 ... (remaining 17310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 7158 15.29 - 30.58: 364 30.58 - 45.86: 70 45.86 - 61.15: 9 61.15 - 76.44: 8 Dihedral angle restraints: 7609 sinusoidal: 2991 harmonic: 4618 Sorted by residual: dihedral pdb=" CA ASN D 450 " pdb=" C ASN D 450 " pdb=" N ASN D 451 " pdb=" CA ASN D 451 " ideal model delta harmonic sigma weight residual 180.00 147.94 32.06 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CA PHE C 170 " pdb=" C PHE C 170 " pdb=" N ASN C 171 " pdb=" CA ASN C 171 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PHE D 434 " pdb=" C PHE D 434 " pdb=" N ARG D 435 " pdb=" CA ARG D 435 " ideal model delta harmonic sigma weight residual 180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 7606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1743 0.078 - 0.156: 207 0.156 - 0.234: 13 0.234 - 0.312: 1 0.312 - 0.390: 4 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CB ILE D 453 " pdb=" CA ILE D 453 " pdb=" CG1 ILE D 453 " pdb=" CG2 ILE D 453 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB VAL D 454 " pdb=" CA VAL D 454 " pdb=" CG1 VAL D 454 " pdb=" CG2 VAL D 454 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB ILE C 172 " pdb=" CA ILE C 172 " pdb=" CG1 ILE C 172 " pdb=" CG2 ILE C 172 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1965 not shown) Planarity restraints: 2161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 508 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C VAL A 508 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 508 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR A 509 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 510 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C LEU A 510 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU A 510 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 511 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 346 " 0.022 2.00e-02 2.50e+03 1.52e-02 5.77e+00 pdb=" CG TRP B 346 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 346 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 346 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 346 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 346 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 346 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 346 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 346 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 346 " 0.004 2.00e-02 2.50e+03 ... (remaining 2158 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3447 2.81 - 3.33: 11373 3.33 - 3.85: 20249 3.85 - 4.38: 23229 4.38 - 4.90: 39733 Nonbonded interactions: 98031 Sorted by model distance: nonbonded pdb=" O PRO B 365 " pdb=" OH TYR B 422 " model vdw 2.283 2.440 nonbonded pdb=" O LYS B 108 " pdb=" OG SER B 111 " model vdw 2.307 2.440 nonbonded pdb=" OH TYR B 158 " pdb=" O HIS B 228 " model vdw 2.316 2.440 nonbonded pdb=" O GLU A 512 " pdb=" OG SER A 515 " model vdw 2.323 2.440 nonbonded pdb=" O LYS A 108 " pdb=" OG SER A 111 " model vdw 2.326 2.440 ... (remaining 98026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 54 through 316 or (resid 317 and (name N or name CA or nam \ e C or name O or name CB )) or resid 339 through 608)) selection = (chain 'B' and (resid 54 through 388 or (resid 389 and (name N or name CA or nam \ e C or name O or name CB )) or resid 390 or (resid 391 through 392 and (name N o \ r name CA or name C or name O or name CB )) or resid 393 through 608)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.430 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: 0.000 Extract box with map and model: 2.210 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.550 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.004 0.062 12766 Z= 0.287 Angle : 0.900 13.688 17315 Z= 0.499 Chirality : 0.053 0.390 1968 Planarity : 0.007 0.056 2161 Dihedral : 10.187 76.440 4593 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 0.45 % Allowed : 3.35 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.46 (0.17), residues: 1523 helix: -1.78 (0.13), residues: 930 sheet: -2.19 (0.61), residues: 65 loop : -3.05 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP B 346 HIS 0.004 0.001 HIS D 108 PHE 0.030 0.003 PHE B 398 TYR 0.032 0.002 TYR D 21 ARG 0.006 0.001 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 448 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8540 (pt) cc_final: 0.8205 (mt) REVERT: A 137 TYR cc_start: 0.6828 (m-10) cc_final: 0.5795 (m-10) REVERT: A 179 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7290 (tm) REVERT: A 307 ARG cc_start: 0.8503 (mmp80) cc_final: 0.8213 (mmp-170) REVERT: B 96 THR cc_start: 0.8413 (m) cc_final: 0.8073 (p) REVERT: B 126 TYR cc_start: 0.7354 (p90) cc_final: 0.7132 (p90) REVERT: B 133 ILE cc_start: 0.7500 (tt) cc_final: 0.6603 (tt) REVERT: B 534 TYR cc_start: 0.7738 (m-80) cc_final: 0.7420 (m-80) REVERT: B 608 SER cc_start: 0.8035 (m) cc_final: 0.7539 (p) REVERT: C 88 GLN cc_start: 0.7991 (tt0) cc_final: 0.7583 (tm-30) REVERT: C 92 GLU cc_start: 0.7133 (tt0) cc_final: 0.6778 (tm-30) REVERT: C 107 ASP cc_start: 0.8207 (t0) cc_final: 0.7880 (t0) REVERT: C 157 MET cc_start: 0.8261 (mtp) cc_final: 0.7898 (mtp) REVERT: D 141 TRP cc_start: 0.7927 (p-90) cc_final: 0.7531 (p-90) REVERT: D 275 LYS cc_start: 0.8375 (mttp) cc_final: 0.8117 (mtpp) REVERT: D 399 PHE cc_start: 0.7206 (t80) cc_final: 0.6969 (t80) outliers start: 6 outliers final: 1 residues processed: 452 average time/residue: 0.2714 time to fit residues: 168.5640 Evaluate side-chains 243 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain D residue 476 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 116 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 406 GLN A 474 GLN A 543 ASN A 598 GLN B 67 ASN B 394 ASN B 543 ASN C 142 ASN ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 404 ASN D 443 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12766 Z= 0.239 Angle : 0.636 10.009 17315 Z= 0.327 Chirality : 0.043 0.229 1968 Planarity : 0.005 0.049 2161 Dihedral : 5.324 35.851 1685 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.72 % Allowed : 11.54 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.43 (0.20), residues: 1523 helix: 0.01 (0.16), residues: 969 sheet: -1.47 (0.70), residues: 57 loop : -2.77 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 346 HIS 0.009 0.001 HIS C 96 PHE 0.022 0.002 PHE A 264 TYR 0.021 0.002 TYR D 21 ARG 0.007 0.001 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 250 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6223 (mmm160) cc_final: 0.5987 (mmm160) REVERT: A 119 MET cc_start: 0.6646 (ttp) cc_final: 0.6277 (ttp) REVERT: A 130 ILE cc_start: 0.8469 (pt) cc_final: 0.8193 (mt) REVERT: A 137 TYR cc_start: 0.6424 (m-10) cc_final: 0.6019 (m-10) REVERT: A 179 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7078 (tm) REVERT: A 307 ARG cc_start: 0.8463 (mmp80) cc_final: 0.8135 (mmp-170) REVERT: A 343 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8026 (t) REVERT: A 554 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6396 (mm-30) REVERT: B 96 THR cc_start: 0.8441 (m) cc_final: 0.8005 (p) REVERT: B 126 TYR cc_start: 0.7364 (p90) cc_final: 0.7077 (p90) REVERT: B 474 GLN cc_start: 0.7301 (tp-100) cc_final: 0.6723 (tm-30) REVERT: B 534 TYR cc_start: 0.7577 (m-80) cc_final: 0.7230 (m-80) REVERT: B 608 SER cc_start: 0.8024 (m) cc_final: 0.7530 (p) REVERT: C 88 GLN cc_start: 0.7994 (tt0) cc_final: 0.7597 (tm-30) REVERT: C 157 MET cc_start: 0.8353 (mtp) cc_final: 0.8139 (mtp) REVERT: D 141 TRP cc_start: 0.8046 (p-90) cc_final: 0.7532 (p-90) REVERT: D 275 LYS cc_start: 0.8530 (mttp) cc_final: 0.8221 (mtpp) REVERT: D 325 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.5812 (tm) outliers start: 50 outliers final: 34 residues processed: 287 average time/residue: 0.2339 time to fit residues: 97.7992 Evaluate side-chains 244 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 207 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN B 67 ASN B 303 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12766 Z= 0.153 Angle : 0.562 9.848 17315 Z= 0.285 Chirality : 0.040 0.225 1968 Planarity : 0.004 0.049 2161 Dihedral : 4.866 36.318 1685 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.10 % Allowed : 13.48 % Favored : 82.43 % 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: -0.38 (0.22), residues: 1523 helix: 0.93 (0.17), residues: 951 sheet: -1.08 (0.73), residues: 57 loop : -2.46 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 65 HIS 0.004 0.001 HIS D 439 PHE 0.017 0.001 PHE A 101 TYR 0.018 0.001 TYR A 301 ARG 0.004 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 246 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6636 (ttp) cc_final: 0.6368 (ttp) REVERT: A 130 ILE cc_start: 0.8465 (pt) cc_final: 0.8131 (mt) REVERT: A 137 TYR cc_start: 0.6379 (m-10) cc_final: 0.5962 (m-10) REVERT: A 179 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7078 (tm) REVERT: A 256 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8683 (mp) REVERT: A 428 LEU cc_start: 0.8005 (tt) cc_final: 0.7532 (tt) REVERT: B 96 THR cc_start: 0.8298 (m) cc_final: 0.7861 (p) REVERT: B 474 GLN cc_start: 0.7141 (tp-100) cc_final: 0.6624 (tm-30) REVERT: B 534 TYR cc_start: 0.7696 (m-80) cc_final: 0.7318 (m-80) REVERT: B 608 SER cc_start: 0.7973 (m) cc_final: 0.7470 (p) REVERT: C 88 GLN cc_start: 0.8014 (tt0) cc_final: 0.7633 (tm-30) REVERT: D 141 TRP cc_start: 0.7827 (p-90) cc_final: 0.7415 (p-90) REVERT: D 275 LYS cc_start: 0.8476 (mttp) cc_final: 0.8178 (mtpp) REVERT: D 325 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5668 (tm) outliers start: 55 outliers final: 35 residues processed: 278 average time/residue: 0.2217 time to fit residues: 92.0404 Evaluate side-chains 245 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12766 Z= 0.267 Angle : 0.635 11.530 17315 Z= 0.321 Chirality : 0.043 0.257 1968 Planarity : 0.004 0.046 2161 Dihedral : 4.948 38.044 1685 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.10 % Allowed : 15.93 % Favored : 79.97 % 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: -0.22 (0.22), residues: 1523 helix: 1.05 (0.17), residues: 953 sheet: -1.23 (0.73), residues: 57 loop : -2.35 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 346 HIS 0.006 0.001 HIS B 262 PHE 0.027 0.002 PHE B 64 TYR 0.017 0.002 TYR B 345 ARG 0.003 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 214 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6676 (ttp) cc_final: 0.6308 (ttp) REVERT: A 130 ILE cc_start: 0.8569 (pt) cc_final: 0.8217 (mt) REVERT: A 137 TYR cc_start: 0.6422 (m-10) cc_final: 0.6017 (m-10) REVERT: A 179 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7266 (tm) REVERT: A 256 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8797 (mp) REVERT: A 376 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: A 428 LEU cc_start: 0.8064 (tt) cc_final: 0.7625 (tt) REVERT: B 474 GLN cc_start: 0.7294 (tp-100) cc_final: 0.6798 (tm-30) REVERT: C 88 GLN cc_start: 0.7971 (tt0) cc_final: 0.7736 (tm-30) REVERT: D 141 TRP cc_start: 0.7990 (p-90) cc_final: 0.7515 (p-90) REVERT: D 275 LYS cc_start: 0.8576 (mttp) cc_final: 0.8111 (mtpp) REVERT: D 325 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5721 (tm) outliers start: 55 outliers final: 42 residues processed: 250 average time/residue: 0.2045 time to fit residues: 77.3628 Evaluate side-chains 235 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12766 Z= 0.189 Angle : 0.593 10.712 17315 Z= 0.298 Chirality : 0.041 0.224 1968 Planarity : 0.004 0.045 2161 Dihedral : 4.794 38.039 1685 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.77 % Allowed : 15.19 % Favored : 80.04 % 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 (0.22), residues: 1523 helix: 1.32 (0.17), residues: 956 sheet: -0.71 (0.66), residues: 71 loop : -2.32 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 346 HIS 0.004 0.001 HIS D 439 PHE 0.024 0.002 PHE B 64 TYR 0.026 0.001 TYR B 345 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 211 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6722 (ttp) cc_final: 0.6383 (ttp) REVERT: A 130 ILE cc_start: 0.8490 (pt) cc_final: 0.8169 (mt) REVERT: A 137 TYR cc_start: 0.6340 (m-10) cc_final: 0.5982 (m-10) REVERT: A 179 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7280 (tm) REVERT: A 256 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8785 (mp) REVERT: A 343 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.7894 (t) REVERT: A 376 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: A 428 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7843 (mt) REVERT: B 474 GLN cc_start: 0.7147 (tp-100) cc_final: 0.6789 (tm-30) REVERT: C 88 GLN cc_start: 0.7973 (tt0) cc_final: 0.7765 (tm-30) REVERT: D 123 LEU cc_start: 0.8456 (mm) cc_final: 0.8230 (mp) REVERT: D 141 TRP cc_start: 0.7937 (p-90) cc_final: 0.7536 (p-90) REVERT: D 325 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5654 (tm) REVERT: D 396 ASP cc_start: 0.3668 (m-30) cc_final: 0.3350 (m-30) outliers start: 64 outliers final: 46 residues processed: 249 average time/residue: 0.1969 time to fit residues: 75.5728 Evaluate side-chains 244 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 0.0010 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN D 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12766 Z= 0.324 Angle : 0.669 11.980 17315 Z= 0.340 Chirality : 0.044 0.258 1968 Planarity : 0.004 0.045 2161 Dihedral : 5.059 42.433 1685 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 5.44 % Allowed : 16.23 % Favored : 78.33 % 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: -0.10 (0.22), residues: 1523 helix: 1.12 (0.17), residues: 962 sheet: -1.39 (0.72), residues: 57 loop : -2.31 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 65 HIS 0.007 0.001 HIS B 262 PHE 0.022 0.002 PHE A 264 TYR 0.022 0.002 TYR B 345 ARG 0.005 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 197 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6647 (ttp) cc_final: 0.6179 (ttp) REVERT: A 130 ILE cc_start: 0.8568 (pt) cc_final: 0.8245 (mt) REVERT: A 137 TYR cc_start: 0.6340 (m-10) cc_final: 0.5965 (m-10) REVERT: A 179 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7299 (tm) REVERT: A 256 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8875 (mp) REVERT: A 376 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: A 476 PHE cc_start: 0.8514 (m-80) cc_final: 0.8167 (m-10) REVERT: B 446 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7441 (m-80) REVERT: B 474 GLN cc_start: 0.7325 (tp-100) cc_final: 0.7026 (tm-30) REVERT: B 592 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7260 (p) REVERT: C 88 GLN cc_start: 0.8032 (tt0) cc_final: 0.7783 (tm-30) REVERT: D 123 LEU cc_start: 0.8517 (mm) cc_final: 0.8279 (mp) REVERT: D 141 TRP cc_start: 0.8037 (p-90) cc_final: 0.7642 (p-90) REVERT: D 325 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6030 (tm) REVERT: D 434 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7917 (t80) outliers start: 73 outliers final: 54 residues processed: 244 average time/residue: 0.1984 time to fit residues: 73.9204 Evaluate side-chains 250 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 189 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 434 PHE Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 125 optimal weight: 0.0870 chunk 83 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 12766 Z= 0.157 Angle : 0.590 11.947 17315 Z= 0.297 Chirality : 0.041 0.259 1968 Planarity : 0.003 0.041 2161 Dihedral : 4.752 42.631 1685 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.87 % Allowed : 17.72 % Favored : 78.41 % 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: 0.39 (0.22), residues: 1523 helix: 1.57 (0.17), residues: 948 sheet: -1.19 (0.71), residues: 57 loop : -2.15 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 412 HIS 0.004 0.001 HIS D 439 PHE 0.022 0.001 PHE B 64 TYR 0.023 0.001 TYR B 345 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 219 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8526 (pt) cc_final: 0.8186 (mt) REVERT: A 137 TYR cc_start: 0.6339 (m-10) cc_final: 0.6049 (m-10) REVERT: A 179 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7265 (tm) REVERT: A 343 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.7821 (t) REVERT: A 376 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: A 476 PHE cc_start: 0.8418 (m-80) cc_final: 0.7968 (m-10) REVERT: B 474 GLN cc_start: 0.7082 (tp-100) cc_final: 0.6799 (tm-30) REVERT: B 608 SER cc_start: 0.7980 (m) cc_final: 0.7517 (p) REVERT: C 21 LYS cc_start: 0.7679 (mmtt) cc_final: 0.7448 (mmmt) REVERT: C 88 GLN cc_start: 0.7973 (tt0) cc_final: 0.7725 (tm-30) REVERT: D 123 LEU cc_start: 0.8507 (mm) cc_final: 0.8303 (mp) REVERT: D 141 TRP cc_start: 0.7836 (p-90) cc_final: 0.7572 (p-90) REVERT: D 325 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5782 (tm) REVERT: D 434 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7965 (t80) outliers start: 52 outliers final: 36 residues processed: 248 average time/residue: 0.1990 time to fit residues: 76.0115 Evaluate side-chains 237 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 434 PHE Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 0.0570 chunk 135 optimal weight: 5.9990 overall best weight: 0.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12766 Z= 0.143 Angle : 0.586 14.196 17315 Z= 0.292 Chirality : 0.040 0.207 1968 Planarity : 0.003 0.040 2161 Dihedral : 4.553 42.796 1685 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.87 % Allowed : 18.24 % Favored : 77.89 % 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 (0.22), residues: 1523 helix: 1.73 (0.17), residues: 954 sheet: -1.04 (0.70), residues: 57 loop : -2.12 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 346 HIS 0.004 0.001 HIS D 439 PHE 0.021 0.001 PHE B 64 TYR 0.022 0.001 TYR B 345 ARG 0.009 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 214 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6733 (ttp) cc_final: 0.6162 (ttp) REVERT: A 130 ILE cc_start: 0.8525 (pt) cc_final: 0.8072 (mt) REVERT: A 137 TYR cc_start: 0.6250 (m-10) cc_final: 0.5961 (m-10) REVERT: A 179 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7224 (tm) REVERT: A 343 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8129 (t) REVERT: B 222 GLN cc_start: 0.8614 (mt0) cc_final: 0.8413 (tt0) REVERT: B 226 MET cc_start: 0.8887 (mmt) cc_final: 0.8478 (tpt) REVERT: B 353 ARG cc_start: 0.8091 (ttp-170) cc_final: 0.7826 (ttp-110) REVERT: B 608 SER cc_start: 0.8075 (m) cc_final: 0.7555 (p) REVERT: C 21 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7383 (mmmt) REVERT: D 123 LEU cc_start: 0.8520 (mm) cc_final: 0.8317 (mp) REVERT: D 141 TRP cc_start: 0.7805 (p-90) cc_final: 0.7568 (p-90) REVERT: D 325 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5713 (tm) REVERT: D 335 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.6732 (mp10) REVERT: D 434 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7833 (t80) outliers start: 52 outliers final: 36 residues processed: 245 average time/residue: 0.2004 time to fit residues: 74.5824 Evaluate side-chains 235 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 434 PHE Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 0.0470 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 427 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12766 Z= 0.188 Angle : 0.630 14.986 17315 Z= 0.314 Chirality : 0.042 0.231 1968 Planarity : 0.004 0.040 2161 Dihedral : 4.569 38.543 1685 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.95 % Allowed : 18.76 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1523 helix: 1.69 (0.17), residues: 955 sheet: -0.98 (0.70), residues: 57 loop : -2.10 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 346 HIS 0.004 0.001 HIS D 439 PHE 0.022 0.001 PHE A 476 TYR 0.032 0.001 TYR B 345 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 197 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.6945 (mtm) cc_final: 0.6742 (mpp) REVERT: A 119 MET cc_start: 0.6685 (ttp) cc_final: 0.6093 (ttp) REVERT: A 130 ILE cc_start: 0.8560 (pt) cc_final: 0.8126 (mt) REVERT: A 137 TYR cc_start: 0.6277 (m-10) cc_final: 0.5983 (m-10) REVERT: A 179 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7333 (tm) REVERT: A 343 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8075 (t) REVERT: A 476 PHE cc_start: 0.8438 (m-80) cc_final: 0.8100 (m-10) REVERT: B 353 ARG cc_start: 0.8185 (ttp-170) cc_final: 0.7748 (ttp-110) REVERT: C 21 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7363 (mmmt) REVERT: D 141 TRP cc_start: 0.7819 (p-90) cc_final: 0.7563 (p-90) REVERT: D 325 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5794 (tm) REVERT: D 335 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.6869 (mp10) REVERT: D 434 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7926 (t80) outliers start: 53 outliers final: 39 residues processed: 231 average time/residue: 0.2165 time to fit residues: 75.3118 Evaluate side-chains 237 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 193 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 434 PHE Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12766 Z= 0.178 Angle : 0.633 15.991 17315 Z= 0.316 Chirality : 0.042 0.233 1968 Planarity : 0.004 0.040 2161 Dihedral : 4.533 38.847 1685 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.80 % Allowed : 18.84 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.56 (0.22), residues: 1523 helix: 1.66 (0.17), residues: 953 sheet: -0.87 (0.71), residues: 57 loop : -2.05 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 412 HIS 0.004 0.001 HIS D 439 PHE 0.019 0.001 PHE B 500 TYR 0.028 0.001 TYR B 345 ARG 0.006 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 201 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6555 (ttp) cc_final: 0.5969 (ttp) REVERT: A 130 ILE cc_start: 0.8567 (pt) cc_final: 0.8133 (mt) REVERT: A 137 TYR cc_start: 0.6238 (m-10) cc_final: 0.5924 (m-10) REVERT: A 179 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7268 (tm) REVERT: A 343 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8089 (t) REVERT: A 376 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: A 461 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: A 476 PHE cc_start: 0.8376 (m-80) cc_final: 0.8075 (m-10) REVERT: B 353 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7741 (ttp-110) REVERT: C 21 LYS cc_start: 0.7571 (mmtt) cc_final: 0.7303 (mmmt) REVERT: D 325 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5800 (tm) REVERT: D 335 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.6867 (mp10) outliers start: 51 outliers final: 37 residues processed: 232 average time/residue: 0.2131 time to fit residues: 76.5102 Evaluate side-chains 235 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN D 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114714 restraints weight = 21895.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117338 restraints weight = 13753.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119067 restraints weight = 10121.292| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12766 Z= 0.217 Angle : 0.645 16.076 17315 Z= 0.325 Chirality : 0.043 0.235 1968 Planarity : 0.004 0.039 2161 Dihedral : 4.600 38.916 1685 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.65 % Allowed : 18.76 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.52 (0.22), residues: 1523 helix: 1.62 (0.17), residues: 955 sheet: -0.96 (0.71), residues: 57 loop : -2.06 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 141 HIS 0.004 0.001 HIS D 439 PHE 0.020 0.002 PHE B 500 TYR 0.027 0.002 TYR B 345 ARG 0.006 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2509.03 seconds wall clock time: 48 minutes 8.19 seconds (2888.19 seconds total)