Starting phenix.real_space_refine on Mon Aug 25 10:08:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmq_19367/08_2025/8rmq_19367.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmq_19367/08_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_19367/08_2025/8rmq_19367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmq_19367/08_2025/8rmq_19367.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmq_19367/08_2025/8rmq_19367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmq_19367/08_2025/8rmq_19367.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.99, per 1000 atoms: 0.15 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: 1.83 Conformation dependent library (CDL) restraints added in 657.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.64 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: 5.23 Time building geometry restraints manager: 2.42 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: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.820 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- 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 : 4.54 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG A 196 TYR 0.012 0.001 TYR B 555 PHE 0.015 0.001 PHE B 505 TRP 0.008 0.001 TRP B 438 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00276 (13933) covalent geometry : angle 0.48488 (18778) hydrogen bonds : bond 0.13279 ( 718) hydrogen bonds : angle 5.82657 ( 1989) *********************** 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 : 0.628 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: 1.3254 time to fit residues: 331.1959 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 : 0.742 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0020 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.164554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130474 restraints weight = 42562.233| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.63 r_work: 0.3352 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13933 Z= 0.146 Angle : 0.512 5.907 18778 Z= 0.279 Chirality : 0.039 0.162 2050 Planarity : 0.004 0.041 2418 Dihedral : 8.011 82.399 1922 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.20), residues: 1680 helix: 1.63 (0.18), residues: 819 sheet: 0.02 (0.37), residues: 204 loop : -0.42 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.013 0.001 TYR B 555 PHE 0.015 0.001 PHE B 505 TRP 0.009 0.001 TRP B 309 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00324 (13933) covalent geometry : angle 0.51191 (18778) hydrogen bonds : bond 0.05157 ( 718) hydrogen bonds : angle 5.02860 ( 1989) *********************** 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 235 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7485 (ttt) REVERT: A 312 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7903 (mtmt) REVERT: A 604 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: B 104 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: B 180 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7407 (tt0) outliers start: 40 outliers final: 21 residues processed: 227 average time/residue: 1.2699 time to fit residues: 314.3495 Evaluate side-chains 214 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 188 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 193 GLN A 222 ASN B 116 GLN B 284 ASN B 313 GLN B 346 ASN B 545 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129401 restraints weight = 42373.687| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.63 r_work: 0.3338 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13933 Z= 0.156 Angle : 0.515 7.673 18778 Z= 0.278 Chirality : 0.039 0.151 2050 Planarity : 0.004 0.048 2418 Dihedral : 5.964 65.327 1877 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 20.48 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.20), residues: 1680 helix: 1.60 (0.18), residues: 819 sheet: -0.17 (0.38), residues: 198 loop : -0.54 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.013 0.001 TYR B 555 PHE 0.017 0.001 PHE B 505 TRP 0.010 0.001 TRP B 438 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00361 (13933) covalent geometry : angle 0.51523 (18778) hydrogen bonds : bond 0.05205 ( 718) hydrogen bonds : angle 4.89648 ( 1989) *********************** 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 241 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7478 (ttt) REVERT: A 120 ILE cc_start: 0.8475 (mt) cc_final: 0.8179 (mp) REVERT: A 170 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7687 (mtm110) REVERT: A 306 ASP cc_start: 0.7807 (m-30) cc_final: 0.7583 (m-30) REVERT: A 604 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: B 104 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: B 180 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: B 311 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: B 387 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6268 (tp30) REVERT: B 688 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7759 (ptm) REVERT: C 6 GLU cc_start: 0.7714 (tp30) cc_final: 0.7502 (tp30) REVERT: C 241 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8236 (tp30) outliers start: 37 outliers final: 18 residues processed: 234 average time/residue: 1.3552 time to fit residues: 344.4224 Evaluate side-chains 225 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 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 533 ASN 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 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 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 117 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 222 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 = 0.3869 r_free = 0.3869 target = 0.164289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130436 restraints weight = 42167.070| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.61 r_work: 0.3344 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13933 Z= 0.130 Angle : 0.493 6.346 18778 Z= 0.266 Chirality : 0.038 0.150 2050 Planarity : 0.004 0.043 2418 Dihedral : 5.671 59.177 1874 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 2.58 % Allowed : 19.55 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1680 helix: 1.65 (0.18), residues: 822 sheet: -0.17 (0.38), residues: 198 loop : -0.53 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 508 TYR 0.012 0.001 TYR B 555 PHE 0.015 0.001 PHE B 505 TRP 0.009 0.001 TRP B 438 HIS 0.011 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00294 (13933) covalent geometry : angle 0.49258 (18778) hydrogen bonds : bond 0.04756 ( 718) hydrogen bonds : angle 4.78164 ( 1989) *********************** 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 247 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7451 (ttt) REVERT: A 252 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: A 604 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: B 104 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: B 112 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7123 (mp0) REVERT: B 311 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: B 387 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6150 (tp30) REVERT: B 742 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6151 (tm-30) REVERT: C 6 GLU cc_start: 0.7681 (tp30) cc_final: 0.7447 (tp30) REVERT: C 241 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8206 (tp30) outliers start: 39 outliers final: 18 residues processed: 240 average time/residue: 1.2920 time to fit residues: 338.0595 Evaluate side-chains 223 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 157 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 469 LEU 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 A residue 613 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 104 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 67 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 156 optimal weight: 0.3980 chunk 81 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.163068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.128911 restraints weight = 42257.831| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.63 r_work: 0.3332 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13933 Z= 0.159 Angle : 0.512 6.818 18778 Z= 0.277 Chirality : 0.039 0.153 2050 Planarity : 0.004 0.051 2418 Dihedral : 5.498 59.020 1869 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 2.92 % Allowed : 19.42 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.20), residues: 1680 helix: 1.57 (0.18), residues: 822 sheet: -0.29 (0.38), residues: 199 loop : -0.57 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 508 TYR 0.013 0.001 TYR B 555 PHE 0.019 0.001 PHE B 505 TRP 0.010 0.001 TRP B 438 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00370 (13933) covalent geometry : angle 0.51217 (18778) hydrogen bonds : bond 0.05047 ( 718) hydrogen bonds : angle 4.79889 ( 1989) *********************** 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 246 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7507 (ttt) REVERT: A 120 ILE cc_start: 0.8464 (mp) cc_final: 0.7934 (mp) REVERT: A 170 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7695 (mtm110) REVERT: A 252 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: A 604 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: B 104 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: B 387 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6244 (tp30) REVERT: B 742 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6009 (tm-30) REVERT: C 6 GLU cc_start: 0.7712 (tp30) cc_final: 0.7499 (tp30) REVERT: C 241 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8256 (tp30) outliers start: 44 outliers final: 21 residues processed: 239 average time/residue: 1.4079 time to fit residues: 364.4299 Evaluate side-chains 221 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 252 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 67 ILE 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 124 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 158 optimal weight: 0.1980 chunk 127 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS A 193 GLN A 222 ASN 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 = 0.3865 r_free = 0.3865 target = 0.164079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129953 restraints weight = 42469.245| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.64 r_work: 0.3340 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1065 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= 0.125 Angle : 0.488 6.422 18778 Z= 0.263 Chirality : 0.038 0.149 2050 Planarity : 0.004 0.048 2418 Dihedral : 4.837 58.380 1864 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 2.19 % Allowed : 20.15 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.20), residues: 1680 helix: 1.68 (0.18), residues: 822 sheet: -0.26 (0.38), residues: 199 loop : -0.51 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 508 TYR 0.012 0.001 TYR B 555 PHE 0.014 0.001 PHE B 505 TRP 0.009 0.001 TRP B 438 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00285 (13933) covalent geometry : angle 0.48807 (18778) hydrogen bonds : bond 0.04630 ( 718) hydrogen bonds : angle 4.69632 ( 1989) *********************** 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 238 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7436 (ttt) REVERT: A 144 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.7117 (t-170) REVERT: A 252 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: A 469 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8322 (tt) REVERT: A 508 ARG cc_start: 0.7075 (ttm110) cc_final: 0.6858 (ttm110) REVERT: B 104 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: B 371 GLU cc_start: 0.7352 (mp0) cc_final: 0.7140 (mp0) REVERT: B 387 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6155 (tp30) REVERT: B 687 GLN cc_start: 0.7710 (mm110) cc_final: 0.7497 (mm110) REVERT: B 742 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6095 (tm-30) REVERT: C 6 GLU cc_start: 0.7702 (tp30) cc_final: 0.7468 (tp30) REVERT: C 142 ARG cc_start: 0.6547 (mtt180) cc_final: 0.4842 (pmt170) REVERT: C 241 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8259 (tp30) outliers start: 33 outliers final: 19 residues processed: 230 average time/residue: 1.3767 time to fit residues: 344.4712 Evaluate side-chains 223 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 144 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 67 ILE 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 99 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS A 193 GLN A 222 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 = 0.3876 r_free = 0.3876 target = 0.164878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.131065 restraints weight = 42073.960| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.64 r_work: 0.3354 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13933 Z= 0.117 Angle : 0.482 6.212 18778 Z= 0.260 Chirality : 0.038 0.147 2050 Planarity : 0.004 0.059 2418 Dihedral : 4.532 57.994 1858 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 2.19 % Allowed : 20.21 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.20), residues: 1680 helix: 1.72 (0.18), residues: 827 sheet: -0.03 (0.40), residues: 179 loop : -0.62 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.012 0.001 TYR B 555 PHE 0.013 0.001 PHE B 505 TRP 0.008 0.001 TRP B 438 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00266 (13933) covalent geometry : angle 0.48224 (18778) hydrogen bonds : bond 0.04466 ( 718) hydrogen bonds : angle 4.63673 ( 1989) *********************** 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 236 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7431 (ttt) REVERT: A 170 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7663 (mtm110) REVERT: A 252 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: A 469 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8355 (tt) REVERT: A 508 ARG cc_start: 0.7105 (ttm110) cc_final: 0.6889 (ttm110) REVERT: B 1 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7227 (tmt) REVERT: B 104 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: B 112 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6369 (mt-10) REVERT: B 350 ARG cc_start: 0.8355 (ttt-90) cc_final: 0.7809 (ttt-90) REVERT: B 387 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6184 (tp30) REVERT: B 742 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6087 (tm-30) REVERT: C 6 GLU cc_start: 0.7720 (tp30) cc_final: 0.7500 (tp30) REVERT: C 28 MET cc_start: 0.8345 (tmt) cc_final: 0.7654 (tmt) REVERT: C 241 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8290 (tp30) outliers start: 33 outliers final: 17 residues processed: 226 average time/residue: 1.4016 time to fit residues: 343.0842 Evaluate side-chains 220 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 252 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 67 ILE 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 12 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 B 533 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.164750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130210 restraints weight = 42369.898| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.60 r_work: 0.3358 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1163 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 : 0.484 6.186 18778 Z= 0.260 Chirality : 0.038 0.147 2050 Planarity : 0.004 0.047 2418 Dihedral : 4.416 57.747 1856 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 1.92 % Allowed : 20.61 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.20), residues: 1680 helix: 1.72 (0.18), residues: 827 sheet: 0.00 (0.40), residues: 179 loop : -0.60 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.012 0.001 TYR B 555 PHE 0.014 0.001 PHE B 505 TRP 0.008 0.001 TRP B 438 HIS 0.006 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00277 (13933) covalent geometry : angle 0.48394 (18778) hydrogen bonds : bond 0.04462 ( 718) hydrogen bonds : angle 4.61276 ( 1989) *********************** 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 229 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7407 (ttt) REVERT: A 170 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7631 (mtm110) REVERT: A 252 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: A 469 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8327 (tt) REVERT: B 1 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7298 (tmt) REVERT: B 104 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: B 112 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6351 (mt-10) REVERT: B 350 ARG cc_start: 0.8372 (ttt-90) cc_final: 0.7802 (ttt-90) REVERT: B 387 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6151 (tp30) REVERT: B 742 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6205 (tm-30) REVERT: C 6 GLU cc_start: 0.7704 (tp30) cc_final: 0.7477 (tp30) REVERT: C 28 MET cc_start: 0.8338 (tmt) cc_final: 0.7650 (tmt) REVERT: C 241 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8236 (tp30) outliers start: 29 outliers final: 13 residues processed: 220 average time/residue: 1.3184 time to fit residues: 314.3098 Evaluate side-chains 214 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 252 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 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 147 optimal weight: 0.0980 chunk 137 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 66 optimal weight: 0.0470 chunk 35 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 B 533 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132653 restraints weight = 42264.261| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.64 r_work: 0.3369 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13933 Z= 0.102 Angle : 0.469 5.637 18778 Z= 0.251 Chirality : 0.037 0.143 2050 Planarity : 0.004 0.067 2418 Dihedral : 4.310 56.869 1855 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 1.79 % Allowed : 21.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.21), residues: 1680 helix: 1.88 (0.18), residues: 826 sheet: 0.19 (0.41), residues: 168 loop : -0.59 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 508 TYR 0.011 0.001 TYR B 555 PHE 0.010 0.001 PHE B 505 TRP 0.008 0.001 TRP A 577 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00229 (13933) covalent geometry : angle 0.46918 (18778) hydrogen bonds : bond 0.04056 ( 718) hydrogen bonds : angle 4.51577 ( 1989) *********************** 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 224 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7413 (ttt) REVERT: A 120 ILE cc_start: 0.8277 (mp) cc_final: 0.7720 (mp) REVERT: A 170 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7637 (mtm110) REVERT: A 252 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: A 469 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8332 (tt) REVERT: A 513 ASN cc_start: 0.6423 (p0) cc_final: 0.6121 (p0) REVERT: B 104 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: B 112 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6369 (mt-10) REVERT: B 350 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.7826 (ttt-90) REVERT: B 387 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6141 (tp30) REVERT: B 742 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6223 (tm-30) REVERT: C 6 GLU cc_start: 0.7725 (tp30) cc_final: 0.7504 (tp30) REVERT: C 28 MET cc_start: 0.8331 (tmt) cc_final: 0.7649 (tmt) REVERT: C 90 MET cc_start: 0.7591 (mmm) cc_final: 0.7150 (mmm) outliers start: 27 outliers final: 11 residues processed: 217 average time/residue: 1.5507 time to fit residues: 365.0046 Evaluate side-chains 211 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 252 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 188 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 147 optimal weight: 0.0370 chunk 98 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 B 533 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.165666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131940 restraints weight = 42386.669| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.61 r_work: 0.3373 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13933 Z= 0.114 Angle : 0.479 5.925 18778 Z= 0.257 Chirality : 0.037 0.146 2050 Planarity : 0.004 0.042 2418 Dihedral : 4.318 56.818 1855 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 1.39 % Allowed : 21.47 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.21), residues: 1680 helix: 1.86 (0.18), residues: 827 sheet: 0.09 (0.40), residues: 167 loop : -0.58 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 170 TYR 0.012 0.001 TYR B 555 PHE 0.014 0.001 PHE B 505 TRP 0.008 0.001 TRP B 438 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00262 (13933) covalent geometry : angle 0.47878 (18778) hydrogen bonds : bond 0.04234 ( 718) hydrogen bonds : angle 4.51484 ( 1989) ********************** 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 218 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7397 (ttt) REVERT: A 170 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7635 (mtm110) REVERT: A 252 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: A 469 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8361 (tt) REVERT: A 513 ASN cc_start: 0.6504 (p0) cc_final: 0.6208 (p0) REVERT: B 104 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: B 112 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.5950 (mp0) REVERT: B 350 ARG cc_start: 0.8373 (ttt-90) cc_final: 0.7834 (ttt-90) REVERT: B 387 GLU cc_start: 0.6627 (mm-30) cc_final: 0.6135 (tp30) REVERT: B 742 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6163 (tm-30) REVERT: C 6 GLU cc_start: 0.7733 (tp30) cc_final: 0.7522 (tp30) REVERT: C 90 MET cc_start: 0.7606 (mmm) cc_final: 0.7165 (mmm) outliers start: 21 outliers final: 12 residues processed: 210 average time/residue: 1.7165 time to fit residues: 390.7718 Evaluate side-chains 212 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 252 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 188 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 133 optimal weight: 0.0980 chunk 102 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 B 533 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.164840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131002 restraints weight = 42165.225| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.63 r_work: 0.3350 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13933 Z= 0.126 Angle : 0.492 6.222 18778 Z= 0.264 Chirality : 0.038 0.147 2050 Planarity : 0.004 0.042 2418 Dihedral : 4.368 56.684 1855 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.33 % Allowed : 21.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.20), residues: 1680 helix: 1.79 (0.18), residues: 827 sheet: 0.08 (0.40), residues: 167 loop : -0.61 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 170 TYR 0.013 0.001 TYR B 555 PHE 0.018 0.001 PHE B 505 TRP 0.009 0.001 TRP B 438 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00293 (13933) covalent geometry : angle 0.49165 (18778) hydrogen bonds : bond 0.04450 ( 718) hydrogen bonds : angle 4.54264 ( 1989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9579.12 seconds wall clock time: 162 minutes 35.03 seconds (9755.03 seconds total)