Starting phenix.real_space_refine on Mon Jun 23 13:08:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmq_19367/06_2025/8rmq_19367.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmq_19367/06_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_19367/06_2025/8rmq_19367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmq_19367/06_2025/8rmq_19367.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmq_19367/06_2025/8rmq_19367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmq_19367/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.82, per 1000 atoms: 0.51 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: 7.41 Conformation dependent library (CDL) restraints added in 2.2 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: 2.29 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: 11.44 Time building geometry restraints manager: 9.06 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: 6.630 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: 0.480 Extract box with map and model: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 59.830 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 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:12.140 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.910 ------------------------------------------------------------------------------- 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 : 3.281 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: 3.2620 time to fit residues: 820.9294 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 : 2.760 ------------------------------------------------------------------------------- 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 = 0.129945 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 : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7484 (ttt) REVERT: A 312 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7908 (mtmt) REVERT: A 604 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: B 104 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: B 180 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7418 (tt0) outliers start: 40 outliers final: 22 residues processed: 228 average time/residue: 3.2847 time to fit residues: 826.0343 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 : 2.152 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 0.0470 overall best weight: 1.6084 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.162453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128057 restraints weight = 42189.248| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.64 r_work: 0.3317 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13933 Z= 0.194 Angle : 0.552 8.210 18778 Z= 0.299 Chirality : 0.040 0.154 2050 Planarity : 0.005 0.049 2418 Dihedral : 6.371 67.004 1880 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.05 % Allowed : 19.95 % Favored : 77.00 % 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: 0.60 (0.20), residues: 1680 helix: 1.42 (0.18), residues: 819 sheet: -0.25 (0.37), residues: 202 loop : -0.63 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 438 HIS 0.006 0.001 HIS B 47 PHE 0.021 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 0.05663 ( 718) hydrogen bonds : angle 4.98271 ( 1989) covalent geometry : bond 0.00455 (13933) covalent geometry : angle 0.55171 (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 250 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7480 (ttt) REVERT: A 170 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7665 (mtm110) REVERT: A 306 ASP cc_start: 0.7858 (m-30) cc_final: 0.7628 (m-30) REVERT: A 604 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: B 104 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: B 180 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: B 311 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: B 371 GLU cc_start: 0.7380 (mp0) cc_final: 0.7171 (mp0) REVERT: B 387 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6302 (tp30) REVERT: B 688 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7788 (ptm) REVERT: C 6 GLU cc_start: 0.7781 (tp30) cc_final: 0.7562 (tp30) REVERT: C 241 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8230 (tp30) outliers start: 46 outliers final: 21 residues processed: 240 average time/residue: 3.0405 time to fit residues: 794.3154 Evaluate side-chains 227 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 2.175 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 89 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.162358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127392 restraints weight = 42633.680| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.62 r_work: 0.3326 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13933 Z= 0.184 Angle : 0.540 7.162 18778 Z= 0.293 Chirality : 0.040 0.156 2050 Planarity : 0.005 0.046 2418 Dihedral : 5.996 63.638 1875 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.11 % Allowed : 19.35 % 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: 0.47 (0.20), residues: 1680 helix: 1.32 (0.18), residues: 824 sheet: -0.13 (0.38), residues: 192 loop : -0.80 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 438 HIS 0.005 0.001 HIS B 47 PHE 0.020 0.001 PHE B 505 TYR 0.013 0.002 TYR B 555 ARG 0.004 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.05435 ( 718) hydrogen bonds : angle 4.92354 ( 1989) covalent geometry : bond 0.00429 (13933) covalent geometry : angle 0.53981 (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 254 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7435 (ttt) REVERT: A 302 ILE cc_start: 0.7782 (mt) cc_final: 0.7313 (mp) REVERT: A 604 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: B 104 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: B 180 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: B 311 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: B 371 GLU cc_start: 0.7365 (mp0) cc_final: 0.7087 (mp0) REVERT: B 387 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6272 (tp30) REVERT: B 687 GLN cc_start: 0.7815 (mm110) cc_final: 0.7600 (mm110) REVERT: C 6 GLU cc_start: 0.7753 (tp30) cc_final: 0.7544 (tp30) REVERT: C 241 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8238 (tp30) outliers start: 47 outliers final: 24 residues processed: 244 average time/residue: 3.0625 time to fit residues: 814.0556 Evaluate side-chains 229 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 1.990 ------------------------------------------------------------------------------- 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 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 518 VAL 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 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 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 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 Chi-restraints excluded: chain C residue 735 MET 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: 0.0970 chunk 17 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 105 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 116 GLN B 284 ASN B 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.164113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130167 restraints weight = 42470.742| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.63 r_work: 0.3343 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1030 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= 0.116 Angle : 0.487 6.219 18778 Z= 0.263 Chirality : 0.038 0.147 2050 Planarity : 0.004 0.056 2418 Dihedral : 5.423 58.242 1872 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 2.65 % Allowed : 19.62 % Favored : 77.73 % 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: 1.58 (0.18), residues: 826 sheet: -0.06 (0.39), residues: 189 loop : -0.70 (0.23), residues: 665 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 0.012 0.001 PHE B 505 TYR 0.011 0.001 TYR B 555 ARG 0.007 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 718) hydrogen bonds : angle 4.74593 ( 1989) covalent geometry : bond 0.00257 (13933) covalent geometry : angle 0.48728 (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 258 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7442 (ttt) REVERT: A 144 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.7106 (t-170) REVERT: A 170 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7659 (mtm110) REVERT: A 302 ILE cc_start: 0.7798 (mt) cc_final: 0.7372 (mp) REVERT: A 469 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8329 (tt) REVERT: A 604 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8068 (mm-30) REVERT: B 104 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: B 112 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6424 (mt-10) REVERT: B 311 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: B 350 ARG cc_start: 0.8365 (ttt-90) cc_final: 0.7788 (ttt-90) REVERT: B 371 GLU cc_start: 0.7364 (mp0) cc_final: 0.7156 (mp0) REVERT: B 387 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6162 (tp30) REVERT: B 687 GLN cc_start: 0.7721 (mm110) cc_final: 0.7442 (mm110) REVERT: C 6 GLU cc_start: 0.7711 (tp30) cc_final: 0.7460 (tp30) REVERT: C 90 MET cc_start: 0.7565 (mmm) cc_final: 0.7121 (mmm) REVERT: C 241 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8240 (tp30) outliers start: 40 outliers final: 21 residues processed: 251 average time/residue: 3.0475 time to fit residues: 833.0904 Evaluate side-chains 226 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 2.495 ------------------------------------------------------------------------------- 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 144 HIS Chi-restraints excluded: chain A residue 157 THR 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 19 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 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 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: 1.9990 chunk 11 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 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: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3858 r_free = 0.3858 target = 0.163322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129365 restraints weight = 42366.300| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.64 r_work: 0.3334 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1102 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= 0.143 Angle : 0.506 6.571 18778 Z= 0.273 Chirality : 0.038 0.150 2050 Planarity : 0.005 0.072 2418 Dihedral : 5.323 58.285 1869 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 2.05 % Allowed : 20.74 % Favored : 77.20 % 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: 1.55 (0.18), residues: 828 sheet: -0.11 (0.39), residues: 189 loop : -0.69 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.018 0.001 HIS A 144 PHE 0.017 0.001 PHE B 505 TYR 0.013 0.001 TYR B 555 ARG 0.012 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 718) hydrogen bonds : angle 4.74679 ( 1989) covalent geometry : bond 0.00333 (13933) covalent geometry : angle 0.50603 (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 228 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7432 (ttt) REVERT: A 128 HIS cc_start: 0.7423 (p-80) cc_final: 0.7128 (p-80) REVERT: A 469 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8370 (tt) REVERT: A 508 ARG cc_start: 0.7055 (ttm110) cc_final: 0.6826 (ttm110) REVERT: B 104 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: B 112 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6379 (mt-10) REVERT: B 311 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8370 (mt-10) REVERT: B 350 ARG cc_start: 0.8390 (ttt-90) cc_final: 0.7826 (ttt-90) REVERT: B 371 GLU cc_start: 0.7371 (mp0) cc_final: 0.7151 (mp0) REVERT: B 387 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6200 (tp30) REVERT: B 687 GLN cc_start: 0.7786 (mm110) cc_final: 0.7504 (mm110) REVERT: C 6 GLU cc_start: 0.7723 (tp30) cc_final: 0.7489 (tp30) REVERT: C 90 MET cc_start: 0.7577 (mmm) cc_final: 0.7136 (mmm) REVERT: C 241 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8256 (tp30) outliers start: 31 outliers final: 18 residues processed: 222 average time/residue: 3.1381 time to fit residues: 759.4889 Evaluate side-chains 216 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 3.522 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 71 optimal weight: 1.9990 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: 0.9980 chunk 164 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 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 A 222 ASN B 116 GLN B 284 ASN B 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128179 restraints weight = 42214.244| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.64 r_work: 0.3352 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1152 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= 0.143 Angle : 0.505 6.642 18778 Z= 0.272 Chirality : 0.038 0.149 2050 Planarity : 0.005 0.060 2418 Dihedral : 4.953 57.976 1861 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 2.65 % Allowed : 20.01 % Favored : 77.34 % 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: 1.55 (0.18), residues: 827 sheet: -0.10 (0.39), residues: 190 loop : -0.69 (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 B 47 PHE 0.017 0.001 PHE B 505 TYR 0.013 0.001 TYR B 555 ARG 0.010 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.04850 ( 718) hydrogen bonds : angle 4.72321 ( 1989) covalent geometry : bond 0.00330 (13933) covalent geometry : angle 0.50511 (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 238 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7394 (ttt) REVERT: A 128 HIS cc_start: 0.7366 (p-80) cc_final: 0.7064 (p-80) REVERT: A 170 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7637 (mtm110) REVERT: A 469 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8348 (tt) REVERT: A 599 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6445 (tp30) REVERT: B 104 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: B 112 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6352 (mt-10) REVERT: B 350 ARG cc_start: 0.8402 (ttt-90) cc_final: 0.7825 (ttt-90) REVERT: B 371 GLU cc_start: 0.7363 (mp0) cc_final: 0.7132 (mp0) REVERT: B 387 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6189 (tp30) REVERT: C 6 GLU cc_start: 0.7683 (tp30) cc_final: 0.7457 (tp30) REVERT: C 28 MET cc_start: 0.8336 (tmt) cc_final: 0.7635 (tmt) REVERT: C 241 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8195 (tp30) outliers start: 40 outliers final: 22 residues processed: 230 average time/residue: 3.9676 time to fit residues: 995.4002 Evaluate side-chains 224 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 3.197 ------------------------------------------------------------------------------- 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 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 599 GLU Chi-restraints excluded: chain A residue 613 GLU 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 520 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 B residue 735 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 135 optimal weight: 0.0970 chunk 81 optimal weight: 0.0470 chunk 87 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 146 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131769 restraints weight = 42326.799| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.63 r_work: 0.3359 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13933 Z= 0.104 Angle : 0.474 5.828 18778 Z= 0.254 Chirality : 0.037 0.144 2050 Planarity : 0.004 0.063 2418 Dihedral : 4.492 57.069 1858 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 1.92 % Allowed : 20.81 % Favored : 77.27 % 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: 0.95 (0.21), residues: 1680 helix: 1.77 (0.18), residues: 826 sheet: 0.03 (0.40), residues: 179 loop : -0.61 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.003 0.000 HIS B 47 PHE 0.011 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 0.04202 ( 718) hydrogen bonds : angle 4.59612 ( 1989) covalent geometry : bond 0.00231 (13933) covalent geometry : angle 0.47381 (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 228 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7390 (ttt) REVERT: A 120 ILE cc_start: 0.8254 (mp) cc_final: 0.7681 (mp) REVERT: A 128 HIS cc_start: 0.7337 (p-80) cc_final: 0.7049 (p-80) REVERT: A 170 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7613 (mtm110) REVERT: A 469 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8351 (tt) REVERT: A 508 ARG cc_start: 0.7051 (ttm110) cc_final: 0.6842 (ttm110) REVERT: A 513 ASN cc_start: 0.6517 (p0) cc_final: 0.6190 (p0) REVERT: B 104 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: B 112 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6377 (mt-10) REVERT: B 350 ARG cc_start: 0.8343 (ttt-90) cc_final: 0.7781 (ttt-90) REVERT: B 371 GLU cc_start: 0.7370 (mp0) cc_final: 0.7141 (mp0) REVERT: B 387 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6143 (tp30) REVERT: C 6 GLU cc_start: 0.7705 (tp30) cc_final: 0.7477 (tp30) REVERT: C 28 MET cc_start: 0.8308 (tmt) cc_final: 0.7625 (tmt) REVERT: C 90 MET cc_start: 0.7576 (mmm) cc_final: 0.7143 (mmm) REVERT: C 241 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8288 (tp30) outliers start: 29 outliers final: 10 residues processed: 221 average time/residue: 2.9985 time to fit residues: 720.2932 Evaluate side-chains 208 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 1.978 ------------------------------------------------------------------------------- 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 469 LEU 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 533 ASN 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 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: 2.9990 chunk 35 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 222 ASN B 116 GLN B 124 GLN B 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128281 restraints weight = 42292.547| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.65 r_work: 0.3350 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1226 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= 0.140 Angle : 0.499 6.428 18778 Z= 0.269 Chirality : 0.038 0.148 2050 Planarity : 0.004 0.055 2418 Dihedral : 4.479 57.579 1855 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 1.46 % Allowed : 21.47 % 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: 0.87 (0.20), residues: 1680 helix: 1.67 (0.18), residues: 827 sheet: 0.12 (0.40), residues: 179 loop : -0.63 (0.23), residues: 674 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 0.018 0.001 PHE B 505 TYR 0.013 0.001 TYR B 555 ARG 0.008 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 718) hydrogen bonds : angle 4.64447 ( 1989) covalent geometry : bond 0.00327 (13933) covalent geometry : angle 0.49944 (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 223 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7409 (ttt) REVERT: A 128 HIS cc_start: 0.7318 (p-80) cc_final: 0.6998 (p-80) REVERT: A 170 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7578 (mtm110) REVERT: A 302 ILE cc_start: 0.7821 (mt) cc_final: 0.7447 (mp) REVERT: A 469 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8318 (tt) REVERT: A 508 ARG cc_start: 0.7035 (ttm110) cc_final: 0.6806 (ttm110) REVERT: A 513 ASN cc_start: 0.6528 (p0) cc_final: 0.6212 (p0) REVERT: B 104 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: B 112 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6403 (mt-10) REVERT: B 350 ARG cc_start: 0.8397 (ttt-90) cc_final: 0.7825 (ttt-90) REVERT: B 371 GLU cc_start: 0.7338 (mp0) cc_final: 0.7085 (mp0) REVERT: B 387 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6108 (tp30) REVERT: C 6 GLU cc_start: 0.7702 (tp30) cc_final: 0.7460 (tp30) REVERT: C 28 MET cc_start: 0.8330 (tmt) cc_final: 0.7632 (tmt) REVERT: C 90 MET cc_start: 0.7562 (mmm) cc_final: 0.7116 (mmm) REVERT: C 241 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8233 (tp30) outliers start: 22 outliers final: 12 residues processed: 218 average time/residue: 3.2171 time to fit residues: 764.5125 Evaluate side-chains 214 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 2.252 ------------------------------------------------------------------------------- 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 469 LEU 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 533 ASN 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 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: 5.9990 chunk 164 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 222 ASN B 116 GLN B 284 ASN B 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129855 restraints weight = 42266.906| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.64 r_work: 0.3336 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13933 Z= 0.129 Angle : 0.496 6.391 18778 Z= 0.266 Chirality : 0.038 0.148 2050 Planarity : 0.004 0.054 2418 Dihedral : 4.466 57.199 1855 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.39 % Allowed : 21.60 % Favored : 77.00 % 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: 1.68 (0.18), residues: 827 sheet: -0.02 (0.39), residues: 190 loop : -0.60 (0.23), residues: 663 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 0.013 0.001 TYR B 555 ARG 0.008 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 718) hydrogen bonds : angle 4.62169 ( 1989) covalent geometry : bond 0.00297 (13933) covalent geometry : angle 0.49574 (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 215 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7429 (ttt) REVERT: A 120 ILE cc_start: 0.8291 (mp) cc_final: 0.7720 (mp) REVERT: A 128 HIS cc_start: 0.7326 (p-80) cc_final: 0.7010 (p-80) REVERT: A 252 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 302 ILE cc_start: 0.7855 (mt) cc_final: 0.7478 (mp) REVERT: A 469 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8332 (tt) REVERT: A 508 ARG cc_start: 0.7043 (ttm110) cc_final: 0.6821 (ttm110) REVERT: A 513 ASN cc_start: 0.6538 (p0) cc_final: 0.6208 (p0) REVERT: B 104 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: B 112 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: B 350 ARG cc_start: 0.8394 (ttt-90) cc_final: 0.7822 (ttt-90) REVERT: B 371 GLU cc_start: 0.7344 (mp0) cc_final: 0.7094 (mp0) REVERT: B 387 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6145 (tp30) REVERT: C 6 GLU cc_start: 0.7755 (tp30) cc_final: 0.7501 (tp30) REVERT: C 28 MET cc_start: 0.8355 (tmt) cc_final: 0.7663 (tmt) REVERT: C 90 MET cc_start: 0.7582 (mmm) cc_final: 0.7138 (mmm) REVERT: C 241 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8231 (tp30) outliers start: 21 outliers final: 13 residues processed: 209 average time/residue: 3.2232 time to fit residues: 730.6945 Evaluate side-chains 213 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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 198 GLU 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 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 533 ASN 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 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: 0.6980 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: 0.9980 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 222 ASN B 116 GLN B 124 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 = 0.3853 r_free = 0.3853 target = 0.162969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128872 restraints weight = 42190.984| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.64 r_work: 0.3323 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13933 Z= 0.153 Angle : 0.515 6.688 18778 Z= 0.277 Chirality : 0.039 0.149 2050 Planarity : 0.005 0.062 2418 Dihedral : 4.532 57.365 1855 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 1.52 % Allowed : 21.47 % Favored : 77.00 % 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: 0.81 (0.20), residues: 1680 helix: 1.61 (0.18), residues: 827 sheet: -0.02 (0.39), residues: 190 loop : -0.63 (0.23), residues: 663 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 0.020 0.001 PHE B 505 TYR 0.013 0.001 TYR B 555 ARG 0.010 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 718) hydrogen bonds : angle 4.66552 ( 1989) covalent geometry : bond 0.00361 (13933) covalent geometry : angle 0.51506 (18778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22977.99 seconds wall clock time: 397 minutes 29.71 seconds (23849.71 seconds total)