Starting phenix.real_space_refine on Sat Apr 6 19:12:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p27_17358/04_2024/8p27_17358_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p27_17358/04_2024/8p27_17358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p27_17358/04_2024/8p27_17358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p27_17358/04_2024/8p27_17358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p27_17358/04_2024/8p27_17358_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p27_17358/04_2024/8p27_17358_updated.pdb" } resolution = 2.73 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= 0.000 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5564 2.51 5 N 1517 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8810 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4372 Classifications: {'peptide': 544} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 523} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4376 Classifications: {'peptide': 545} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 524} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.05, per 1000 atoms: 0.57 Number of scatterers: 8810 At special positions: 0 Unit cell: (101.509, 104.112, 96.3036, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 1667 8.00 N 1517 7.00 C 5564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 5 sheets defined 42.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 122 through 141 removed outlier: 3.714A pdb=" N MET A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 145 through 151 removed outlier: 3.768A pdb=" N ALA A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 197 through 213 removed outlier: 3.899A pdb=" N GLN A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 246 Proline residue: A 230 - end of helix removed outlier: 3.763A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 284 through 298 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 335 through 338 No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.833A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 456 through 485 removed outlier: 3.545A pdb=" N PHE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 499 No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 546 through 549 No H-bonds generated for 'chain 'A' and resid 546 through 549' Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.898A pdb=" N MET A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 594 removed outlier: 4.015A pdb=" N LYS A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 634 Proline residue: A 630 - end of helix removed outlier: 4.954A pdb=" N ASP A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'B' and resid 122 through 141 removed outlier: 3.671A pdb=" N PHE B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix removed outlier: 3.528A pdb=" N ASP B 140 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 197 through 214 removed outlier: 4.346A pdb=" N ASN B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 242 removed outlier: 3.634A pdb=" N LEU B 228 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Proline residue: B 230 - end of helix removed outlier: 3.810A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 298 removed outlier: 3.692A pdb=" N HIS B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 333 removed outlier: 3.572A pdb=" N ILE B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 368 through 378 removed outlier: 3.515A pdb=" N ALA B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 409 Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 456 through 485 removed outlier: 3.688A pdb=" N PHE B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 546 through 569 removed outlier: 3.567A pdb=" N LEU B 552 " --> pdb=" O GLN B 548 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N MET B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 592 removed outlier: 3.597A pdb=" N LYS B 590 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 634 removed outlier: 3.812A pdb=" N ILE B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Proline residue: B 630 - end of helix removed outlier: 4.846A pdb=" N ASP B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU B 634 " --> pdb=" O PRO B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 665 removed outlier: 3.520A pdb=" N GLU B 657 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER B 658 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 661 " --> pdb=" O SER B 658 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 665 " --> pdb=" O MET B 662 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 156 through 158 removed outlier: 7.731A pdb=" N THR A 521 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE A 438 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 523 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N THR A 440 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY A 525 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 526 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.482A pdb=" N ILE A 350 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR A 317 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 352 " --> pdb=" O TYR A 317 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN A 385 " --> pdb=" O TRP A 353 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LYS A 355 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 387 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 156 through 158 removed outlier: 7.675A pdb=" N THR B 521 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE B 438 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY B 523 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR B 440 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY B 525 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 526 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 219 through 221 removed outlier: 3.581A pdb=" N ASN B 316 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 350 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR B 317 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE B 352 " --> pdb=" O TYR B 317 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN B 385 " --> pdb=" O TRP B 353 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LYS B 355 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 387 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 642 through 644 removed outlier: 7.063A pdb=" N SER B 672 " --> pdb=" O VAL B 643 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 248 hydrogen bonds defined for protein. 720 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: 2.14 Time building geometry restraints manager: 3.86 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: 2901 1.34 - 1.46: 1587 1.46 - 1.57: 4420 1.57 - 1.69: 10 1.69 - 1.81: 90 Bond restraints: 9008 Sorted by residual: bond pdb=" CA SER B 304 " pdb=" C SER B 304 " ideal model delta sigma weight residual 1.528 1.516 0.011 1.37e-02 5.33e+03 6.93e-01 bond pdb=" C4' DTP B 801 " pdb=" O4' DTP B 801 " ideal model delta sigma weight residual 1.444 1.436 0.008 1.10e-02 8.26e+03 5.41e-01 bond pdb=" CB GLU A 277 " pdb=" CG GLU A 277 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.84e-01 bond pdb=" CG PRO B 175 " pdb=" CD PRO B 175 " ideal model delta sigma weight residual 1.503 1.480 0.023 3.40e-02 8.65e+02 4.72e-01 bond pdb=" CA LYS A 135 " pdb=" C LYS A 135 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 4.36e-01 ... (remaining 9003 not shown) Histogram of bond angle deviations from ideal: 99.97 - 107.96: 358 107.96 - 115.95: 5474 115.95 - 123.95: 6125 123.95 - 131.94: 206 131.94 - 139.94: 16 Bond angle restraints: 12179 Sorted by residual: angle pdb=" N GLU A 514 " pdb=" CA GLU A 514 " pdb=" C GLU A 514 " ideal model delta sigma weight residual 114.75 110.29 4.46 1.26e+00 6.30e-01 1.25e+01 angle pdb=" N ALA A 535 " pdb=" CA ALA A 535 " pdb=" C ALA A 535 " ideal model delta sigma weight residual 114.16 110.17 3.99 1.48e+00 4.57e-01 7.26e+00 angle pdb=" CA GLU A 514 " pdb=" C GLU A 514 " pdb=" N SER A 515 " ideal model delta sigma weight residual 119.80 116.34 3.46 1.34e+00 5.57e-01 6.67e+00 angle pdb=" C ALA A 391 " pdb=" N THR A 392 " pdb=" CA THR A 392 " ideal model delta sigma weight residual 121.54 125.85 -4.31 1.91e+00 2.74e-01 5.10e+00 angle pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " pdb=" CG TYR A 231 " ideal model delta sigma weight residual 113.90 109.85 4.05 1.80e+00 3.09e-01 5.07e+00 ... (remaining 12174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 4922 15.53 - 31.07: 358 31.07 - 46.60: 101 46.60 - 62.14: 33 62.14 - 77.67: 5 Dihedral angle restraints: 5419 sinusoidal: 2250 harmonic: 3169 Sorted by residual: dihedral pdb=" CA VAL A 534 " pdb=" C VAL A 534 " pdb=" N ALA A 535 " pdb=" CA ALA A 535 " ideal model delta harmonic sigma weight residual 180.00 152.85 27.15 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ASP B 390 " pdb=" C ASP B 390 " pdb=" N ALA B 391 " pdb=" CA ALA B 391 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA VAL B 534 " pdb=" C VAL B 534 " pdb=" N ALA B 535 " pdb=" CA ALA B 535 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 5416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 704 0.030 - 0.061: 392 0.061 - 0.091: 133 0.091 - 0.122: 59 0.122 - 0.152: 12 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA ILE A 524 " pdb=" N ILE A 524 " pdb=" C ILE A 524 " pdb=" CB ILE A 524 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE B 598 " pdb=" N ILE B 598 " pdb=" C ILE B 598 " pdb=" CB ILE B 598 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA VAL A 613 " pdb=" N VAL A 613 " pdb=" C VAL A 613 " pdb=" CB VAL A 613 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1297 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 495 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C LEU A 495 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU A 495 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 496 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 192 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 193 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 362 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 363 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 363 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 363 " 0.019 5.00e-02 4.00e+02 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 44 2.53 - 3.12: 6445 3.12 - 3.71: 12958 3.71 - 4.31: 18321 4.31 - 4.90: 31284 Nonbonded interactions: 69052 Sorted by model distance: nonbonded pdb=" O3B DTP A 801 " pdb="MG MG B 802 " model vdw 1.936 2.170 nonbonded pdb="MG MG A 802 " pdb=" O2B DTP B 801 " model vdw 1.985 2.170 nonbonded pdb="MG MG A 802 " pdb=" O3B DTP B 801 " model vdw 1.985 2.170 nonbonded pdb=" O2B DTP A 801 " pdb="MG MG B 802 " model vdw 2.135 2.170 nonbonded pdb=" O2A DTP A 801 " pdb="MG MG B 802 " model vdw 2.156 2.170 ... (remaining 69047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 120 through 304 or resid 311 through 675 or resid 801 thro \ ugh 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.980 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.440 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 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:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 0.031 9008 Z= 0.239 Angle : 0.551 7.141 12179 Z= 0.298 Chirality : 0.045 0.152 1300 Planarity : 0.004 0.035 1573 Dihedral : 12.492 77.670 3387 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.43 % Allowed : 6.70 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.06 (0.25), residues: 1077 helix: -0.91 (0.23), residues: 504 sheet: 1.09 (0.51), residues: 108 loop : -2.50 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.005 0.001 HIS A 279 PHE 0.015 0.002 PHE A 224 TYR 0.017 0.002 TYR A 231 ARG 0.002 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 293 GLU cc_start: 0.7909 (tt0) cc_final: 0.7629 (tt0) REVERT: A 330 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7342 (ttp-110) REVERT: A 451 MET cc_start: 0.7642 (mtm) cc_final: 0.7387 (mtp) REVERT: A 540 HIS cc_start: 0.7885 (p-80) cc_final: 0.7437 (p90) REVERT: A 564 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: B 249 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.5327 (mp0) REVERT: B 277 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6110 (mm-30) REVERT: B 278 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5919 (tm-30) REVERT: B 424 ARG cc_start: 0.7491 (mtt90) cc_final: 0.7206 (mtt-85) REVERT: B 478 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6776 (mt) REVERT: B 534 VAL cc_start: 0.8319 (t) cc_final: 0.8109 (p) REVERT: B 545 GLU cc_start: 0.6883 (tp30) cc_final: 0.6506 (tp30) REVERT: B 560 ASP cc_start: 0.7821 (m-30) cc_final: 0.7604 (m-30) outliers start: 51 outliers final: 25 residues processed: 276 average time/residue: 1.1163 time to fit residues: 330.1349 Evaluate side-chains 236 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 206 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.0040 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.1980 chunk 98 optimal weight: 0.9980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 367 ASN A 609 ASN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN B 367 ASN B 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9008 Z= 0.188 Angle : 0.537 8.039 12179 Z= 0.287 Chirality : 0.044 0.143 1300 Planarity : 0.004 0.048 1573 Dihedral : 9.791 71.993 1308 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.96 % Allowed : 13.51 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.25), residues: 1077 helix: -0.48 (0.24), residues: 501 sheet: 1.29 (0.50), residues: 108 loop : -2.52 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.005 0.001 HIS A 279 PHE 0.017 0.001 PHE A 184 TYR 0.019 0.001 TYR A 231 ARG 0.002 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 202 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.7233 (mt) cc_final: 0.7012 (mt) REVERT: A 283 LYS cc_start: 0.8289 (ttmm) cc_final: 0.8047 (mtpp) REVERT: A 451 MET cc_start: 0.7586 (mtm) cc_final: 0.7327 (mtp) REVERT: A 505 GLU cc_start: 0.6376 (pp20) cc_final: 0.6037 (pp20) REVERT: A 529 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7745 (tp) REVERT: B 169 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7494 (mp) REVERT: B 277 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5757 (mm-30) REVERT: B 278 GLN cc_start: 0.5790 (OUTLIER) cc_final: 0.5416 (tp-100) REVERT: B 334 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6961 (mt0) REVERT: B 478 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6739 (mt) REVERT: B 545 GLU cc_start: 0.6711 (tp30) cc_final: 0.6416 (tp30) REVERT: B 560 ASP cc_start: 0.7518 (m-30) cc_final: 0.7262 (m-30) outliers start: 56 outliers final: 26 residues processed: 241 average time/residue: 1.1330 time to fit residues: 292.9380 Evaluate side-chains 234 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 607 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 97 optimal weight: 0.4980 chunk 33 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 298 ASN A 609 ASN A 652 ASN B 297 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9008 Z= 0.261 Angle : 0.571 9.751 12179 Z= 0.302 Chirality : 0.046 0.144 1300 Planarity : 0.004 0.049 1573 Dihedral : 9.295 71.764 1293 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 6.38 % Allowed : 15.85 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.25), residues: 1077 helix: -0.33 (0.24), residues: 493 sheet: 1.31 (0.49), residues: 108 loop : -2.50 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 399 HIS 0.007 0.001 HIS A 279 PHE 0.019 0.002 PHE A 482 TYR 0.018 0.002 TYR B 231 ARG 0.002 0.000 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 208 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7079 (t0) cc_final: 0.6833 (t0) REVERT: A 142 LEU cc_start: 0.7264 (mt) cc_final: 0.7030 (mt) REVERT: A 214 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7502 (mt-10) REVERT: A 271 GLN cc_start: 0.7297 (mp10) cc_final: 0.6919 (mp10) REVERT: A 278 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.5518 (tt0) REVERT: A 451 MET cc_start: 0.7665 (mtm) cc_final: 0.7438 (mtp) REVERT: A 505 GLU cc_start: 0.6526 (pp20) cc_final: 0.6187 (pp20) REVERT: A 529 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7752 (tp) REVERT: B 169 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7550 (mp) REVERT: B 268 ASP cc_start: 0.6710 (t0) cc_final: 0.6438 (t0) REVERT: B 277 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5660 (mm-30) REVERT: B 278 GLN cc_start: 0.5818 (OUTLIER) cc_final: 0.5525 (tp-100) REVERT: B 334 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6968 (mt0) REVERT: B 489 MET cc_start: 0.7743 (mmt) cc_final: 0.7199 (mmt) REVERT: B 545 GLU cc_start: 0.6663 (tp30) cc_final: 0.6430 (tp30) REVERT: B 560 ASP cc_start: 0.7569 (m-30) cc_final: 0.7052 (m-30) outliers start: 60 outliers final: 32 residues processed: 247 average time/residue: 1.1968 time to fit residues: 316.1111 Evaluate side-chains 235 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 197 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 0.0060 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 0.2980 chunk 104 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 609 ASN A 652 ASN B 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9008 Z= 0.185 Angle : 0.521 7.541 12179 Z= 0.277 Chirality : 0.044 0.139 1300 Planarity : 0.004 0.050 1573 Dihedral : 9.064 71.680 1291 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 5.53 % Allowed : 17.98 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.25), residues: 1077 helix: -0.09 (0.24), residues: 488 sheet: 1.48 (0.48), residues: 109 loop : -2.49 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.006 0.001 HIS A 279 PHE 0.018 0.001 PHE A 184 TYR 0.015 0.001 TYR A 231 ARG 0.004 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 204 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7108 (t0) cc_final: 0.6813 (t0) REVERT: A 142 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.7039 (mt) REVERT: A 236 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6472 (t80) REVERT: A 271 GLN cc_start: 0.7260 (mp10) cc_final: 0.6890 (mp10) REVERT: A 451 MET cc_start: 0.7615 (mtm) cc_final: 0.7386 (mtp) REVERT: A 505 GLU cc_start: 0.6533 (pp20) cc_final: 0.6249 (pp20) REVERT: A 529 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7746 (tp) REVERT: B 169 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7482 (mp) REVERT: B 268 ASP cc_start: 0.6671 (t0) cc_final: 0.6399 (t0) REVERT: B 277 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5791 (mm-30) REVERT: B 278 GLN cc_start: 0.5859 (OUTLIER) cc_final: 0.5599 (tp-100) REVERT: B 334 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6939 (mt0) REVERT: B 424 ARG cc_start: 0.7598 (mtt-85) cc_final: 0.7233 (mtt-85) REVERT: B 560 ASP cc_start: 0.7567 (m-30) cc_final: 0.6989 (m-30) REVERT: B 564 GLU cc_start: 0.7296 (mp0) cc_final: 0.7015 (mp0) outliers start: 52 outliers final: 33 residues processed: 239 average time/residue: 1.1128 time to fit residues: 284.8625 Evaluate side-chains 239 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.0010 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 609 ASN A 652 ASN B 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9008 Z= 0.280 Angle : 0.565 6.033 12179 Z= 0.302 Chirality : 0.046 0.141 1300 Planarity : 0.004 0.051 1573 Dihedral : 9.171 76.075 1289 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 6.38 % Allowed : 18.62 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.25), residues: 1077 helix: -0.15 (0.24), residues: 487 sheet: 1.24 (0.54), residues: 91 loop : -2.40 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 399 HIS 0.007 0.001 HIS A 279 PHE 0.021 0.002 PHE A 482 TYR 0.017 0.002 TYR A 231 ARG 0.006 0.001 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 203 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7105 (t0) cc_final: 0.6844 (t0) REVERT: A 236 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6484 (t80) REVERT: A 271 GLN cc_start: 0.7318 (mp10) cc_final: 0.6923 (mp10) REVERT: A 283 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8040 (mtpp) REVERT: A 342 ASN cc_start: 0.7174 (t0) cc_final: 0.6968 (t0) REVERT: A 451 MET cc_start: 0.7688 (mtm) cc_final: 0.7468 (mtp) REVERT: A 505 GLU cc_start: 0.6656 (pp20) cc_final: 0.6370 (pp20) REVERT: A 594 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: B 254 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6921 (mt) REVERT: B 277 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5160 (mp0) REVERT: B 278 GLN cc_start: 0.5912 (OUTLIER) cc_final: 0.5700 (tp-100) REVERT: B 329 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6680 (mtm) REVERT: B 334 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6977 (mt0) REVERT: B 424 ARG cc_start: 0.7623 (mtt-85) cc_final: 0.7262 (mtp85) REVERT: B 560 ASP cc_start: 0.7635 (m-30) cc_final: 0.6843 (m-30) REVERT: B 564 GLU cc_start: 0.7300 (mp0) cc_final: 0.6950 (mp0) outliers start: 60 outliers final: 37 residues processed: 243 average time/residue: 1.1503 time to fit residues: 299.3665 Evaluate side-chains 243 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 199 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.0000 chunk 8 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 609 ASN A 652 ASN B 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9008 Z= 0.196 Angle : 0.532 6.998 12179 Z= 0.282 Chirality : 0.044 0.137 1300 Planarity : 0.004 0.051 1573 Dihedral : 8.994 76.073 1289 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 6.49 % Allowed : 19.04 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.25), residues: 1077 helix: 0.03 (0.24), residues: 484 sheet: 1.50 (0.48), residues: 109 loop : -2.50 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 399 HIS 0.005 0.001 HIS A 279 PHE 0.019 0.001 PHE A 184 TYR 0.016 0.001 TYR A 231 ARG 0.006 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 203 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7098 (t0) cc_final: 0.6883 (t0) REVERT: A 236 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6456 (t80) REVERT: A 271 GLN cc_start: 0.7282 (mp10) cc_final: 0.6879 (mp10) REVERT: A 283 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7999 (mtpp) REVERT: A 342 ASN cc_start: 0.7183 (t0) cc_final: 0.6970 (t0) REVERT: A 451 MET cc_start: 0.7633 (mtm) cc_final: 0.7412 (mtp) REVERT: A 505 GLU cc_start: 0.6607 (pp20) cc_final: 0.6329 (pp20) REVERT: A 529 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7762 (tp) REVERT: B 169 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7501 (mp) REVERT: B 254 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6903 (mt) REVERT: B 277 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5305 (mp0) REVERT: B 329 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6579 (mtm) REVERT: B 334 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6960 (mt0) REVERT: B 560 ASP cc_start: 0.7653 (m-30) cc_final: 0.6812 (m-30) REVERT: B 564 GLU cc_start: 0.7305 (mp0) cc_final: 0.6933 (mp0) outliers start: 61 outliers final: 37 residues processed: 243 average time/residue: 1.1196 time to fit residues: 291.6420 Evaluate side-chains 244 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 200 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 395 GLN A 609 ASN A 652 ASN B 278 GLN B 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9008 Z= 0.339 Angle : 0.607 6.136 12179 Z= 0.326 Chirality : 0.048 0.138 1300 Planarity : 0.004 0.052 1573 Dihedral : 8.959 78.033 1286 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 7.02 % Allowed : 19.68 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.25), residues: 1077 helix: -0.16 (0.24), residues: 487 sheet: 1.30 (0.54), residues: 90 loop : -2.53 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 399 HIS 0.008 0.001 HIS A 279 PHE 0.024 0.002 PHE A 482 TYR 0.018 0.002 TYR A 231 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 203 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7110 (t0) cc_final: 0.6881 (t0) REVERT: A 236 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6506 (t80) REVERT: A 271 GLN cc_start: 0.7351 (mp10) cc_final: 0.6940 (mp10) REVERT: A 278 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6128 (tm-30) REVERT: A 342 ASN cc_start: 0.7230 (t0) cc_final: 0.7005 (t0) REVERT: A 451 MET cc_start: 0.7716 (mtm) cc_final: 0.7482 (mtp) REVERT: A 505 GLU cc_start: 0.6759 (pp20) cc_final: 0.6451 (pp20) REVERT: B 249 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.3994 (mp0) REVERT: B 254 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6963 (mt) REVERT: B 277 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5255 (mp0) REVERT: B 329 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.6698 (mtm) REVERT: B 334 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6969 (mt0) REVERT: B 378 THR cc_start: 0.8654 (t) cc_final: 0.8395 (t) REVERT: B 560 ASP cc_start: 0.7708 (m-30) cc_final: 0.6743 (m-30) REVERT: B 564 GLU cc_start: 0.7320 (mp0) cc_final: 0.7006 (mp0) REVERT: B 576 LEU cc_start: 0.8475 (tp) cc_final: 0.8258 (tp) outliers start: 66 outliers final: 42 residues processed: 245 average time/residue: 1.1427 time to fit residues: 300.5758 Evaluate side-chains 248 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 199 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 395 GLN A 609 ASN A 652 ASN B 278 GLN B 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9008 Z= 0.318 Angle : 0.605 6.175 12179 Z= 0.325 Chirality : 0.048 0.164 1300 Planarity : 0.004 0.052 1573 Dihedral : 8.997 78.227 1286 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 6.60 % Allowed : 19.79 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.25), residues: 1077 helix: -0.20 (0.24), residues: 488 sheet: 1.51 (0.56), residues: 79 loop : -2.50 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 399 HIS 0.005 0.001 HIS A 279 PHE 0.022 0.002 PHE A 184 TYR 0.022 0.002 TYR A 231 ARG 0.005 0.001 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 202 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6231 (pmm) REVERT: A 236 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6478 (t80) REVERT: A 271 GLN cc_start: 0.7342 (mp10) cc_final: 0.6934 (mp10) REVERT: A 342 ASN cc_start: 0.7219 (t0) cc_final: 0.7011 (t0) REVERT: A 451 MET cc_start: 0.7708 (mtm) cc_final: 0.7485 (mtp) REVERT: A 505 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6525 (pp20) REVERT: B 249 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.4060 (mp0) REVERT: B 254 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6991 (mt) REVERT: B 277 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5322 (mp0) REVERT: B 329 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6662 (mtm) REVERT: B 378 THR cc_start: 0.8660 (t) cc_final: 0.8395 (t) REVERT: B 560 ASP cc_start: 0.7707 (m-30) cc_final: 0.7085 (m-30) REVERT: B 564 GLU cc_start: 0.7339 (mp0) cc_final: 0.7114 (mp0) REVERT: B 576 LEU cc_start: 0.8468 (tp) cc_final: 0.8249 (tp) outliers start: 62 outliers final: 43 residues processed: 240 average time/residue: 1.1357 time to fit residues: 292.0218 Evaluate side-chains 254 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 204 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 609 ASN A 652 ASN B 188 HIS B 278 GLN B 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9008 Z= 0.352 Angle : 0.624 6.214 12179 Z= 0.335 Chirality : 0.048 0.163 1300 Planarity : 0.004 0.052 1573 Dihedral : 9.067 78.553 1286 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 6.70 % Allowed : 20.00 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.25), residues: 1077 helix: -0.24 (0.24), residues: 486 sheet: 1.50 (0.56), residues: 79 loop : -2.54 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 399 HIS 0.008 0.001 HIS A 279 PHE 0.023 0.002 PHE A 184 TYR 0.018 0.002 TYR A 231 ARG 0.003 0.000 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 208 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6476 (t80) REVERT: A 271 GLN cc_start: 0.7351 (mp10) cc_final: 0.6945 (mp10) REVERT: A 342 ASN cc_start: 0.7223 (t0) cc_final: 0.7004 (t0) REVERT: A 451 MET cc_start: 0.7720 (mtm) cc_final: 0.7504 (mtp) REVERT: A 505 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6576 (pp20) REVERT: B 249 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.3981 (mp0) REVERT: B 254 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.7004 (mt) REVERT: B 277 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5353 (mp0) REVERT: B 329 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6734 (mtm) REVERT: B 378 THR cc_start: 0.8654 (t) cc_final: 0.8388 (t) REVERT: B 534 VAL cc_start: 0.8321 (t) cc_final: 0.8107 (p) REVERT: B 560 ASP cc_start: 0.7715 (m-30) cc_final: 0.7096 (m-30) REVERT: B 564 GLU cc_start: 0.7337 (mp0) cc_final: 0.7122 (mp0) REVERT: B 576 LEU cc_start: 0.8474 (tp) cc_final: 0.8262 (tp) outliers start: 63 outliers final: 44 residues processed: 247 average time/residue: 1.1146 time to fit residues: 295.0014 Evaluate side-chains 255 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 205 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.0570 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 395 GLN A 609 ASN A 652 ASN B 188 HIS B 278 GLN B 626 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9008 Z= 0.386 Angle : 0.657 7.587 12179 Z= 0.352 Chirality : 0.050 0.181 1300 Planarity : 0.005 0.053 1573 Dihedral : 9.128 79.020 1284 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 5.85 % Allowed : 21.17 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.25), residues: 1077 helix: -0.32 (0.23), residues: 486 sheet: 1.48 (0.56), residues: 79 loop : -2.59 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 399 HIS 0.008 0.001 HIS A 279 PHE 0.024 0.002 PHE A 482 TYR 0.018 0.002 TYR A 231 ARG 0.007 0.001 ARG A 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 204 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6475 (t80) REVERT: A 271 GLN cc_start: 0.7356 (mp10) cc_final: 0.6953 (mp10) REVERT: A 342 ASN cc_start: 0.7224 (t0) cc_final: 0.6999 (t0) REVERT: A 451 MET cc_start: 0.7725 (mtm) cc_final: 0.7510 (mtp) REVERT: A 489 MET cc_start: 0.7308 (mmp) cc_final: 0.6930 (mmt) REVERT: A 505 GLU cc_start: 0.6833 (pp20) cc_final: 0.6597 (pp20) REVERT: B 249 GLU cc_start: 0.5613 (OUTLIER) cc_final: 0.4120 (mp0) REVERT: B 254 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7074 (mt) REVERT: B 277 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5372 (mp0) REVERT: B 329 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6708 (mtm) REVERT: B 378 THR cc_start: 0.8672 (t) cc_final: 0.8384 (t) REVERT: B 534 VAL cc_start: 0.8330 (t) cc_final: 0.8119 (p) REVERT: B 560 ASP cc_start: 0.7720 (m-30) cc_final: 0.7103 (m-30) REVERT: B 564 GLU cc_start: 0.7336 (mp0) cc_final: 0.7130 (mp0) outliers start: 55 outliers final: 45 residues processed: 237 average time/residue: 1.1112 time to fit residues: 282.5458 Evaluate side-chains 253 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 279 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 75 optimal weight: 0.0270 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 395 GLN A 609 ASN A 652 ASN B 626 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.137026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128392 restraints weight = 11850.274| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.54 r_work: 0.3692 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9008 Z= 0.250 Angle : 0.588 6.431 12179 Z= 0.314 Chirality : 0.046 0.161 1300 Planarity : 0.004 0.052 1573 Dihedral : 8.905 78.837 1284 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 5.53 % Allowed : 21.91 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.25), residues: 1077 helix: -0.16 (0.24), residues: 488 sheet: 1.19 (0.55), residues: 91 loop : -2.57 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 399 HIS 0.006 0.001 HIS A 279 PHE 0.025 0.002 PHE A 482 TYR 0.018 0.001 TYR B 231 ARG 0.003 0.000 ARG B 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4744.59 seconds wall clock time: 85 minutes 31.01 seconds (5131.01 seconds total)