Starting phenix.real_space_refine on Sun May 25 18:47:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmq_19367/05_2025/8rmq_19367.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmq_19367/05_2025/8rmq_19367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rmq_19367/05_2025/8rmq_19367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmq_19367/05_2025/8rmq_19367.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmq_19367/05_2025/8rmq_19367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmq_19367/05_2025/8rmq_19367.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.090 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 Mg 2 5.21 5 S 103 5.16 5 C 8631 2.51 5 N 2365 2.21 5 O 2569 1.98 5 H 13647 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27317 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 11418 Classifications: {'peptide': 707} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 674} Chain breaks: 1 Chain: "B" Number of atoms: 11026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 11026 Classifications: {'peptide': 694} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 663} Chain breaks: 4 Chain: "C" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4864 Classifications: {'peptide': 297} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain breaks: 1 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 12.15, per 1000 atoms: 0.44 Number of scatterers: 27317 At special positions: 0 Unit cell: (110.88, 110.04, 138.6, 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 103 16.00 Mg 2 11.99 O 2569 8.00 N 2365 7.00 C 8631 6.00 H 13647 1.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.44 Conformation dependent library (CDL) restraints added in 2.1 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 17 sheets defined 52.6% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.570A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.795A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.538A pdb=" N LYS A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 Proline residue: A 534 - end of helix removed outlier: 3.740A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 3.707A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.924A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 716 removed outlier: 3.725A pdb=" N ARG A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.956A pdb=" N GLY B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.591A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.547A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 291 removed outlier: 4.001A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 Proline residue: B 341 - end of helix removed outlier: 3.606A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 375 removed outlier: 4.228A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 687 through 694 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 713 through 731 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.662A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.403A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 removed outlier: 3.573A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.027A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.701A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.031A pdb=" N LYS C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.752A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.685A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 701 through 705 Processing helix chain 'C' and resid 710 through 714 removed outlier: 3.907A pdb=" N SER C 714 " --> pdb=" O ASN C 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 196 removed outlier: 3.764A pdb=" N ARG A 196 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 199 " --> pdb=" O ARG A 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.225A pdb=" N LYS B 481 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP B 305 " --> pdb=" O LYS B 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.724A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.660A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 11.107A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG A 551 " --> pdb=" O GLY A 555 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.018A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.331A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB2, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB3, first strand: chain 'B' and resid 242 through 244 removed outlier: 4.107A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.588A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.626A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.619A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 694 through 699 removed outlier: 6.574A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS C 699 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 1989 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: 11.32 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13618 1.03 - 1.23: 63 1.23 - 1.42: 5698 1.42 - 1.62: 8024 1.62 - 1.81: 177 Bond restraints: 27580 Sorted by residual: bond pdb=" C VAL B 336 " pdb=" O VAL B 336 " ideal model delta sigma weight residual 1.237 1.253 -0.016 1.13e-02 7.83e+03 1.96e+00 bond pdb=" CB GLU A 23 " pdb=" CG GLU A 23 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CB THR B 6 " pdb=" CG2 THR B 6 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CG1 ILE C 19 " pdb=" CD1 ILE C 19 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 8.00e-01 bond pdb=" CA VAL C 139 " pdb=" CB VAL C 139 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.34e-02 5.57e+03 6.72e-01 ... (remaining 27575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 46514 1.03 - 2.06: 3147 2.06 - 3.09: 141 3.09 - 4.12: 61 4.12 - 5.15: 3 Bond angle restraints: 49866 Sorted by residual: angle pdb=" CA PRO B 29 " pdb=" C PRO B 29 " pdb=" N TYR B 30 " ideal model delta sigma weight residual 116.45 118.73 -2.28 8.50e-01 1.38e+00 7.20e+00 angle pdb=" CA PRO B 29 " pdb=" C PRO B 29 " pdb=" O PRO B 29 " ideal model delta sigma weight residual 121.38 119.31 2.07 7.70e-01 1.69e+00 7.20e+00 angle pdb=" CB GLU A 23 " pdb=" CG GLU A 23 " pdb=" CD GLU A 23 " ideal model delta sigma weight residual 112.60 116.47 -3.87 1.70e+00 3.46e-01 5.17e+00 angle pdb=" C ASP B 446 " pdb=" N PHE B 447 " pdb=" CA PHE B 447 " ideal model delta sigma weight residual 121.85 117.98 3.87 1.77e+00 3.19e-01 4.78e+00 angle pdb=" N GLY B 440 " pdb=" CA GLY B 440 " pdb=" C GLY B 440 " ideal model delta sigma weight residual 111.08 114.31 -3.23 1.62e+00 3.81e-01 3.97e+00 ... (remaining 49861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11308 17.99 - 35.97: 1113 35.97 - 53.96: 380 53.96 - 71.95: 85 71.95 - 89.94: 36 Dihedral angle restraints: 12922 sinusoidal: 7159 harmonic: 5763 Sorted by residual: dihedral pdb=" CA CYS B 693 " pdb=" C CYS B 693 " pdb=" N ASN B 694 " pdb=" CA ASN B 694 " ideal model delta harmonic sigma weight residual 180.00 157.95 22.05 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA TYR A 540 " pdb=" C TYR A 540 " pdb=" N CYS A 541 " pdb=" CA CYS A 541 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ARG B 602 " pdb=" C ARG B 602 " pdb=" N ASN B 603 " pdb=" CA ASN B 603 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 12919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1272 0.028 - 0.056: 541 0.056 - 0.083: 132 0.083 - 0.111: 73 0.111 - 0.139: 32 Chirality restraints: 2050 Sorted by residual: chirality pdb=" CA ILE B 667 " pdb=" N ILE B 667 " pdb=" C ILE B 667 " pdb=" CB ILE B 667 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE B 302 " pdb=" N ILE B 302 " pdb=" C ILE B 302 " pdb=" CB ILE B 302 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE B 606 " pdb=" N ILE B 606 " pdb=" C ILE B 606 " pdb=" CB ILE B 606 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 2047 not shown) Planarity restraints: 4032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 595 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C MET A 595 " 0.028 2.00e-02 2.50e+03 pdb=" O MET A 595 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE A 596 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 219 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 220 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 592 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C ILE A 592 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 592 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A 593 " 0.009 2.00e-02 2.50e+03 ... (remaining 4029 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1338 2.17 - 2.78: 54007 2.78 - 3.39: 78810 3.39 - 3.99: 104199 3.99 - 4.60: 161820 Nonbonded interactions: 400174 Sorted by model distance: nonbonded pdb=" OD2 ASP B 522 " pdb=" HH TYR B 559 " model vdw 1.564 2.450 nonbonded pdb=" O ILE B 113 " pdb=" HG1 THR B 117 " model vdw 1.605 2.450 nonbonded pdb=" OE1 GLU B 575 " pdb=" HE ARG C 101 " model vdw 1.613 2.450 nonbonded pdb=" O PHE A 205 " pdb="HD22 ASN B 335 " model vdw 1.614 2.450 nonbonded pdb=" HG SER B 160 " pdb=" OD2 ASP B 165 " model vdw 1.619 2.450 ... (remaining 400169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 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: 0.410 Extract box with map and model: 0.940 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 55.660 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13933 Z= 0.121 Angle : 0.485 5.155 18778 Z= 0.261 Chirality : 0.037 0.139 2050 Planarity : 0.004 0.053 2418 Dihedral : 18.321 89.937 5339 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.65 % Allowed : 20.74 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.21), residues: 1680 helix: 1.67 (0.19), residues: 801 sheet: 0.09 (0.38), residues: 204 loop : -0.44 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 438 HIS 0.003 0.001 HIS B 47 PHE 0.015 0.001 PHE B 505 TYR 0.012 0.001 TYR B 555 ARG 0.007 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.13279 ( 718) hydrogen bonds : angle 5.82657 ( 1989) covalent geometry : bond 0.00276 (13933) covalent geometry : angle 0.48488 (18778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 690 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 742 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6014 (tm-30) outliers start: 40 outliers final: 36 residues processed: 230 average time/residue: 2.9348 time to fit residues: 736.4402 Evaluate side-chains 227 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 736 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 222 ASN B 16 ASN B 116 GLN B 284 ASN B 346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.164228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129929 restraints weight = 42282.659| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.64 r_work: 0.3338 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13933 Z= 0.149 Angle : 0.514 5.862 18778 Z= 0.279 Chirality : 0.039 0.159 2050 Planarity : 0.004 0.041 2418 Dihedral : 8.049 82.542 1922 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.65 % Allowed : 20.48 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1680 helix: 1.61 (0.18), residues: 819 sheet: -0.03 (0.38), residues: 198 loop : -0.41 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.004 0.001 HIS B 47 PHE 0.016 0.001 PHE B 505 TYR 0.014 0.001 TYR B 555 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.05422 ( 718) hydrogen bonds : angle 5.05918 ( 1989) covalent geometry : bond 0.00340 (13933) covalent geometry : angle 0.51363 (18778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 690 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7486 (ttt) REVERT: A 312 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7902 (mtmt) REVERT: A 604 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: B 104 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: B 180 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7423 (tt0) outliers start: 40 outliers final: 22 residues processed: 228 average time/residue: 2.9439 time to fit residues: 736.8616 Evaluate side-chains 219 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 188 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 41 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 36 optimal weight: 0.0470 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 222 ASN B 116 GLN B 284 ASN B 346 ASN B 545 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.162909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128842 restraints weight = 42131.825| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.62 r_work: 0.3324 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13933 Z= 0.188 Angle : 0.543 7.187 18778 Z= 0.294 Chirality : 0.040 0.156 2050 Planarity : 0.004 0.045 2418 Dihedral : 6.359 67.686 1880 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.05 % Allowed : 19.88 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1680 helix: 1.45 (0.18), residues: 819 sheet: -0.22 (0.37), residues: 202 loop : -0.60 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 438 HIS 0.006 0.001 HIS B 47 PHE 0.020 0.002 PHE B 505 TYR 0.014 0.002 TYR B 555 ARG 0.005 0.001 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.05594 ( 718) hydrogen bonds : angle 4.98507 ( 1989) covalent geometry : bond 0.00442 (13933) covalent geometry : angle 0.54341 (18778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 690 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7469 (ttt) REVERT: A 170 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7649 (mtm110) REVERT: A 604 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: B 104 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: B 180 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: B 311 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: B 387 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6265 (tp30) REVERT: B 688 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7800 (ptm) REVERT: C 6 GLU cc_start: 0.7758 (tp30) cc_final: 0.7531 (tp30) REVERT: C 241 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8226 (tp30) outliers start: 46 outliers final: 22 residues processed: 239 average time/residue: 2.9927 time to fit residues: 778.3274 Evaluate side-chains 229 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 131 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN B 116 GLN B 284 ASN B 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129148 restraints weight = 42675.606| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.63 r_work: 0.3337 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13933 Z= 0.143 Angle : 0.508 6.521 18778 Z= 0.275 Chirality : 0.038 0.151 2050 Planarity : 0.004 0.044 2418 Dihedral : 5.903 60.674 1876 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.78 % Allowed : 19.42 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1680 helix: 1.52 (0.18), residues: 821 sheet: -0.19 (0.38), residues: 198 loop : -0.61 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.004 0.001 HIS B 47 PHE 0.016 0.001 PHE B 505 TYR 0.013 0.001 TYR B 555 ARG 0.003 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 718) hydrogen bonds : angle 4.83473 ( 1989) covalent geometry : bond 0.00327 (13933) covalent geometry : angle 0.50765 (18778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 690 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7448 (ttt) REVERT: A 302 ILE cc_start: 0.7766 (mt) cc_final: 0.7314 (mp) REVERT: A 604 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: B 104 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: B 112 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6375 (mt-10) REVERT: B 180 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: B 311 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8360 (mt-10) REVERT: B 387 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6243 (tp30) REVERT: B 742 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6143 (tm-30) REVERT: C 6 GLU cc_start: 0.7731 (tp30) cc_final: 0.7502 (tp30) REVERT: C 241 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8275 (tp30) outliers start: 42 outliers final: 18 residues processed: 240 average time/residue: 3.0236 time to fit residues: 788.7018 Evaluate side-chains 228 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 30 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN B 116 GLN B 284 ASN B 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.161817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126889 restraints weight = 42378.652| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.60 r_work: 0.3319 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13933 Z= 0.206 Angle : 0.557 7.511 18778 Z= 0.303 Chirality : 0.041 0.159 2050 Planarity : 0.005 0.052 2418 Dihedral : 5.672 61.164 1871 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 2.92 % Allowed : 19.68 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1680 helix: 1.34 (0.18), residues: 820 sheet: -0.17 (0.38), residues: 194 loop : -0.79 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 438 HIS 0.006 0.001 HIS A 713 PHE 0.023 0.002 PHE B 505 TYR 0.014 0.002 TYR B 555 ARG 0.006 0.001 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.05635 ( 718) hydrogen bonds : angle 4.93287 ( 1989) covalent geometry : bond 0.00490 (13933) covalent geometry : angle 0.55695 (18778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 690 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7453 (ttt) REVERT: A 170 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7699 (mtm110) REVERT: A 469 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8387 (tt) REVERT: A 604 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: B 104 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: B 112 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6374 (mt-10) REVERT: B 180 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: B 311 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: B 371 GLU cc_start: 0.7413 (mp0) cc_final: 0.7172 (mp0) REVERT: B 387 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6283 (tp30) REVERT: B 687 GLN cc_start: 0.7767 (mm110) cc_final: 0.7514 (mm110) REVERT: B 742 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.5977 (tm-30) REVERT: C 6 GLU cc_start: 0.7732 (tp30) cc_final: 0.7512 (tp30) REVERT: C 241 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8242 (tp30) outliers start: 44 outliers final: 21 residues processed: 248 average time/residue: 3.0696 time to fit residues: 828.4522 Evaluate side-chains 231 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS A 222 ASN B 284 ASN B 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129804 restraints weight = 42317.467| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.62 r_work: 0.3338 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13933 Z= 0.122 Angle : 0.495 6.253 18778 Z= 0.267 Chirality : 0.038 0.148 2050 Planarity : 0.004 0.052 2418 Dihedral : 5.376 58.130 1871 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 2.52 % Allowed : 19.95 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1680 helix: 1.54 (0.18), residues: 827 sheet: -0.09 (0.39), residues: 189 loop : -0.72 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.003 0.001 HIS B 47 PHE 0.014 0.001 PHE B 505 TYR 0.011 0.001 TYR B 555 ARG 0.009 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 718) hydrogen bonds : angle 4.73898 ( 1989) covalent geometry : bond 0.00276 (13933) covalent geometry : angle 0.49536 (18778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 690 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7379 (ttt) REVERT: A 144 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.7141 (t-170) REVERT: A 469 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B 104 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: B 112 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6350 (mt-10) REVERT: B 311 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: B 350 ARG cc_start: 0.8383 (ttt-90) cc_final: 0.7804 (ttt-90) REVERT: B 371 GLU cc_start: 0.7364 (mp0) cc_final: 0.7134 (mp0) REVERT: B 387 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6155 (tp30) REVERT: B 742 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.5982 (tm-30) REVERT: C 6 GLU cc_start: 0.7719 (tp30) cc_final: 0.7458 (tp30) REVERT: C 28 MET cc_start: 0.8308 (tmt) cc_final: 0.7613 (tmt) REVERT: C 241 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8227 (tp30) outliers start: 38 outliers final: 18 residues processed: 238 average time/residue: 3.0184 time to fit residues: 781.3528 Evaluate side-chains 226 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 71 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS A 144 HIS A 222 ASN B 116 GLN B 284 ASN B 346 ASN B 533 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.163971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129291 restraints weight = 42194.413| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.56 r_work: 0.3356 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13933 Z= 0.135 Angle : 0.503 6.538 18778 Z= 0.271 Chirality : 0.038 0.149 2050 Planarity : 0.004 0.056 2418 Dihedral : 5.042 58.215 1863 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 2.25 % Allowed : 20.34 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1680 helix: 1.56 (0.18), residues: 827 sheet: -0.05 (0.39), residues: 190 loop : -0.68 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.004 0.001 HIS A 146 PHE 0.016 0.001 PHE B 505 TYR 0.012 0.001 TYR B 555 ARG 0.008 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 718) hydrogen bonds : angle 4.70538 ( 1989) covalent geometry : bond 0.00311 (13933) covalent geometry : angle 0.50350 (18778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 690 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7395 (ttt) REVERT: A 128 HIS cc_start: 0.7431 (p-80) cc_final: 0.7137 (p-80) REVERT: A 170 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7665 (mtm110) REVERT: A 469 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8383 (tt) REVERT: A 508 ARG cc_start: 0.7059 (ttm110) cc_final: 0.6832 (ttm110) REVERT: B 1 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7206 (tmt) REVERT: B 104 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: B 112 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6343 (mt-10) REVERT: B 350 ARG cc_start: 0.8388 (ttt-90) cc_final: 0.7829 (ttt-90) REVERT: B 387 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6239 (tp30) REVERT: B 687 GLN cc_start: 0.7740 (mm110) cc_final: 0.7480 (mm110) REVERT: B 742 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.5948 (tm-30) REVERT: C 6 GLU cc_start: 0.7692 (tp30) cc_final: 0.7483 (tp30) REVERT: C 28 MET cc_start: 0.8339 (tmt) cc_final: 0.7657 (tmt) REVERT: C 241 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8199 (tp30) outliers start: 34 outliers final: 19 residues processed: 225 average time/residue: 3.1216 time to fit residues: 761.5735 Evaluate side-chains 223 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 116 GLN B 284 ASN B 346 ASN B 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.163781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128465 restraints weight = 42278.919| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.65 r_work: 0.3363 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13933 Z= 0.130 Angle : 0.495 6.426 18778 Z= 0.267 Chirality : 0.038 0.149 2050 Planarity : 0.004 0.050 2418 Dihedral : 4.621 57.885 1858 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 2.45 % Allowed : 20.48 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1680 helix: 1.59 (0.18), residues: 827 sheet: -0.06 (0.39), residues: 190 loop : -0.65 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.005 0.001 HIS A 144 PHE 0.015 0.001 PHE B 505 TYR 0.012 0.001 TYR B 555 ARG 0.008 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 718) hydrogen bonds : angle 4.66570 ( 1989) covalent geometry : bond 0.00298 (13933) covalent geometry : angle 0.49514 (18778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 690 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7404 (ttt) REVERT: A 128 HIS cc_start: 0.7407 (p-80) cc_final: 0.7079 (p-80) REVERT: A 170 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7642 (mtm110) REVERT: A 202 GLU cc_start: 0.7384 (tp30) cc_final: 0.7184 (tp30) REVERT: A 469 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8367 (tt) REVERT: A 508 ARG cc_start: 0.7043 (ttm110) cc_final: 0.6805 (ttm110) REVERT: B 1 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7325 (tmt) REVERT: B 104 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: B 112 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6326 (mt-10) REVERT: B 350 ARG cc_start: 0.8384 (ttt-90) cc_final: 0.7813 (ttt-90) REVERT: B 387 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6192 (tp30) REVERT: B 687 GLN cc_start: 0.7720 (mm110) cc_final: 0.7432 (mm110) REVERT: B 742 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.5949 (tm-30) REVERT: C 6 GLU cc_start: 0.7711 (tp30) cc_final: 0.7490 (tp30) REVERT: C 28 MET cc_start: 0.8338 (tmt) cc_final: 0.7655 (tmt) REVERT: C 155 SER cc_start: 0.7004 (OUTLIER) cc_final: 0.6729 (t) REVERT: C 241 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8249 (tp30) outliers start: 37 outliers final: 14 residues processed: 232 average time/residue: 2.9902 time to fit residues: 753.3615 Evaluate side-chains 218 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 chunk 117 optimal weight: 0.0870 chunk 164 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 116 GLN B 284 ASN B 346 ASN B 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.164713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130838 restraints weight = 42214.195| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.64 r_work: 0.3351 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13933 Z= 0.112 Angle : 0.485 6.076 18778 Z= 0.260 Chirality : 0.037 0.146 2050 Planarity : 0.005 0.107 2418 Dihedral : 4.533 57.424 1857 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.79 % Allowed : 21.40 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1680 helix: 1.72 (0.18), residues: 826 sheet: 0.19 (0.41), residues: 169 loop : -0.66 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 438 HIS 0.003 0.001 HIS B 562 PHE 0.013 0.001 PHE B 505 TYR 0.012 0.001 TYR B 555 ARG 0.017 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 718) hydrogen bonds : angle 4.59012 ( 1989) covalent geometry : bond 0.00254 (13933) covalent geometry : angle 0.48539 (18778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 690 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7396 (ttt) REVERT: A 120 ILE cc_start: 0.8284 (mp) cc_final: 0.7715 (mp) REVERT: A 128 HIS cc_start: 0.7334 (p-80) cc_final: 0.7008 (p-80) REVERT: A 170 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7615 (mtm110) REVERT: A 252 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: A 469 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8335 (tt) REVERT: A 508 ARG cc_start: 0.7042 (ttm110) cc_final: 0.6816 (ttm110) REVERT: A 513 ASN cc_start: 0.6397 (p0) cc_final: 0.6095 (p0) REVERT: B 104 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: B 112 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6409 (mt-10) REVERT: B 350 ARG cc_start: 0.8373 (ttt-90) cc_final: 0.7803 (ttt-90) REVERT: B 387 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6146 (tp30) REVERT: B 687 GLN cc_start: 0.7677 (mm110) cc_final: 0.7347 (mm110) REVERT: B 742 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6229 (tm-30) REVERT: C 6 GLU cc_start: 0.7718 (tp30) cc_final: 0.7484 (tp30) REVERT: C 28 MET cc_start: 0.8329 (tmt) cc_final: 0.7652 (tmt) REVERT: C 90 MET cc_start: 0.7571 (mmm) cc_final: 0.7125 (mmm) REVERT: C 155 SER cc_start: 0.6962 (OUTLIER) cc_final: 0.6700 (t) REVERT: C 241 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8292 (tp30) outliers start: 27 outliers final: 11 residues processed: 220 average time/residue: 3.0394 time to fit residues: 730.2249 Evaluate side-chains 216 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 103 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 31 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 116 GLN B 124 GLN B 284 ASN B 346 ASN B 533 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.164190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130230 restraints weight = 42304.530| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.64 r_work: 0.3343 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13933 Z= 0.126 Angle : 0.494 6.197 18778 Z= 0.265 Chirality : 0.038 0.148 2050 Planarity : 0.004 0.081 2418 Dihedral : 4.462 57.382 1855 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 1.39 % Allowed : 22.00 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1680 helix: 1.69 (0.18), residues: 827 sheet: 0.18 (0.41), residues: 169 loop : -0.66 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.003 0.001 HIS B 47 PHE 0.017 0.001 PHE B 505 TYR 0.012 0.001 TYR B 555 ARG 0.013 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 718) hydrogen bonds : angle 4.58779 ( 1989) covalent geometry : bond 0.00292 (13933) covalent geometry : angle 0.49449 (18778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 690 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7418 (ttt) REVERT: A 128 HIS cc_start: 0.7327 (p-80) cc_final: 0.7007 (p-80) REVERT: A 252 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: A 469 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8330 (tt) REVERT: A 508 ARG cc_start: 0.7020 (ttm110) cc_final: 0.6793 (ttm110) REVERT: B 1 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7266 (tmt) REVERT: B 104 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: B 112 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6401 (mt-10) REVERT: B 350 ARG cc_start: 0.8390 (ttt-90) cc_final: 0.7852 (ttt-90) REVERT: B 387 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6136 (tp30) REVERT: B 731 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6989 (mt-10) REVERT: B 742 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6172 (tm-30) REVERT: C 6 GLU cc_start: 0.7719 (tp30) cc_final: 0.7481 (tp30) REVERT: C 28 MET cc_start: 0.8355 (tmt) cc_final: 0.7685 (tmt) REVERT: C 90 MET cc_start: 0.7581 (mmm) cc_final: 0.7132 (mmm) REVERT: C 155 SER cc_start: 0.6960 (OUTLIER) cc_final: 0.6698 (t) REVERT: C 241 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8272 (tp30) outliers start: 21 outliers final: 8 residues processed: 213 average time/residue: 3.0880 time to fit residues: 714.5012 Evaluate side-chains 213 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 163 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 116 GLN B 284 ASN B 346 ASN B 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.164574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130267 restraints weight = 42339.508| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.56 r_work: 0.3372 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13933 Z= 0.140 Angle : 0.507 6.492 18778 Z= 0.272 Chirality : 0.038 0.149 2050 Planarity : 0.005 0.079 2418 Dihedral : 4.509 57.252 1855 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 1.46 % Allowed : 22.07 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1680 helix: 1.64 (0.18), residues: 827 sheet: 0.18 (0.41), residues: 169 loop : -0.68 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.004 0.001 HIS B 562 PHE 0.019 0.001 PHE B 505 TYR 0.013 0.001 TYR B 555 ARG 0.013 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 718) hydrogen bonds : angle 4.62137 ( 1989) covalent geometry : bond 0.00326 (13933) covalent geometry : angle 0.50672 (18778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20096.69 seconds wall clock time: 343 minutes 46.81 seconds (20626.81 seconds total)