Starting phenix.real_space_refine on Fri Feb 6 23:12:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ryc_54376/02_2026/9ryc_54376.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ryc_54376/02_2026/9ryc_54376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ryc_54376/02_2026/9ryc_54376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ryc_54376/02_2026/9ryc_54376.map" model { file = "/net/cci-nas-00/data/ceres_data/9ryc_54376/02_2026/9ryc_54376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ryc_54376/02_2026/9ryc_54376.cif" } resolution = 2.93 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= 0.000 sd= 0.044 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: 5 Type Number sf(0) Gaussians S 105 5.16 5 C 9166 2.51 5 N 2505 2.21 5 O 2726 1.98 5 H 13520 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28022 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11529 Classifications: {'peptide': 716} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 10797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 10797 Classifications: {'peptide': 678} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain breaks: 5 Chain: "C" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 4744 Classifications: {'peptide': 289} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 275} Chain breaks: 2 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 952 Classifications: {'peptide': 114} Link IDs: {'TRANS': 113} Time building chain proxies: 3.87, per 1000 atoms: 0.14 Number of scatterers: 28022 At special positions: 0 Unit cell: (136.697, 130.483, 103.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 O 2726 8.00 N 2505 7.00 C 9166 6.00 H 13520 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: 2.10 Conformation dependent library (CDL) restraints added in 587.1 milliseconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3392 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 16 sheets defined 52.8% alpha, 11.9% 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 8 Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 31 through 49 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.505A pdb=" N GLU A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) 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 189 through 194 removed outlier: 3.898A pdb=" N GLN A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 194' Processing helix chain 'A' and resid 211 through 216 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 349 removed outlier: 3.924A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 385 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 533 through 538 removed outlier: 3.671A 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 602 removed outlier: 3.931A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.651A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 657 " --> pdb=" O PRO A 653 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.628A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.846A pdb=" N GLU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.661A pdb=" N ASN B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.669A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 250 through 265 removed outlier: 3.835A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 290 removed outlier: 3.571A pdb=" N VAL B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.646A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.537A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.939A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.581A pdb=" N SER B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 520 through 537 removed outlier: 3.856A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 527 " --> pdb=" O MET B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.521A pdb=" N ASN B 603 " --> pdb=" O ASN B 600 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 600 through 604' Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 687 through 700 removed outlier: 3.676A pdb=" N CYS B 692 " --> pdb=" O MET B 688 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS B 693 " --> pdb=" O TYR B 689 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 694 " --> pdb=" O GLN B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 Processing helix chain 'B' and resid 713 through 733 removed outlier: 3.739A pdb=" N ILE B 728 " --> pdb=" O ILE B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 removed outlier: 3.598A pdb=" N PHE B 740 " --> pdb=" O LYS B 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.035A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 23 removed outlier: 3.527A pdb=" N LEU C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.541A pdb=" N MET C 28 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA C 29 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 42 through 53 removed outlier: 3.509A pdb=" N MET C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.669A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.530A pdb=" N LYS C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 167 Processing helix chain 'C' and resid 168 through 172 removed outlier: 4.250A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.508A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 701 through 705 removed outlier: 3.769A pdb=" N GLY C 705 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 716 removed outlier: 3.813A pdb=" N ASN C 715 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 22 Processing helix chain 'D' and resid 25 through 51 Processing helix chain 'D' and resid 61 through 90 Processing helix chain 'D' and resid 92 through 121 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 removed outlier: 3.739A pdb=" N TYR A 110 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 116 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.878A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 292 removed outlier: 7.232A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N CYS A 541 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL A 322 " --> pdb=" O CYS A 541 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N LEU A 543 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE A 545 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.388A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.661A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 366 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 391 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.441A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 244 Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.770A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.495A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 148 removed outlier: 3.622A pdb=" N ILE C 141 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 694 through 699 removed outlier: 6.488A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS C 699 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 2040 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: 6.01 Time building geometry restraints manager: 3.00 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: 13493 1.03 - 1.23: 30 1.23 - 1.42: 6103 1.42 - 1.61: 8495 1.61 - 1.81: 183 Bond restraints: 28304 Sorted by residual: bond pdb=" CA ASP A 389 " pdb=" CB ASP A 389 " ideal model delta sigma weight residual 1.524 1.575 -0.051 1.62e-02 3.81e+03 9.93e+00 bond pdb=" C GLU A 677 " pdb=" O GLU A 677 " ideal model delta sigma weight residual 1.235 1.229 0.006 4.70e-03 4.53e+04 1.79e+00 bond pdb=" CG1 ILE D 80 " pdb=" CD1 ILE D 80 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.48e+00 bond pdb=" N ILE A 138 " pdb=" CA ILE A 138 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.09e+00 bond pdb=" CA VAL C 231 " pdb=" CB VAL C 231 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.06e+00 ... (remaining 28299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 47801 1.13 - 2.27: 2723 2.27 - 3.40: 127 3.40 - 4.53: 54 4.53 - 5.66: 7 Bond angle restraints: 50712 Sorted by residual: angle pdb=" C SER A 140 " pdb=" CA SER A 140 " pdb=" CB SER A 140 " ideal model delta sigma weight residual 116.54 111.25 5.29 1.15e+00 7.56e-01 2.12e+01 angle pdb=" N SER A 388 " pdb=" CA SER A 388 " pdb=" CB SER A 388 " ideal model delta sigma weight residual 114.17 110.07 4.10 1.14e+00 7.69e-01 1.29e+01 angle pdb=" CA MET A 477 " pdb=" C MET A 477 " pdb=" N ASP A 478 " ideal model delta sigma weight residual 116.84 122.50 -5.66 1.71e+00 3.42e-01 1.10e+01 angle pdb=" N SER C 226 " pdb=" CA SER C 226 " pdb=" CB SER C 226 " ideal model delta sigma weight residual 114.17 110.72 3.45 1.14e+00 7.69e-01 9.14e+00 angle pdb=" N SER C 36 " pdb=" CA SER C 36 " pdb=" C SER C 36 " ideal model delta sigma weight residual 111.96 107.78 4.18 1.41e+00 5.03e-01 8.79e+00 ... (remaining 50707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 12157 17.76 - 35.52: 923 35.52 - 53.28: 227 53.28 - 71.04: 77 71.04 - 88.80: 18 Dihedral angle restraints: 13402 sinusoidal: 7352 harmonic: 6050 Sorted by residual: dihedral pdb=" CA ARG D 51 " pdb=" C ARG D 51 " pdb=" N MET D 52 " pdb=" CA MET D 52 " ideal model delta harmonic sigma weight residual 180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+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 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA SER C 226 " pdb=" C SER C 226 " pdb=" N VAL C 227 " pdb=" CA VAL C 227 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 13399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1278 0.027 - 0.055: 648 0.055 - 0.082: 150 0.082 - 0.109: 65 0.109 - 0.137: 31 Chirality restraints: 2172 Sorted by residual: 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 2.57 -0.14 2.00e-01 2.50e+01 4.68e-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 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE B 475 " pdb=" N ILE B 475 " pdb=" C ILE B 475 " pdb=" CB ILE B 475 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 2169 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 309 " 0.016 2.00e-02 2.50e+03 1.22e-02 5.98e+00 pdb=" CG TRP B 309 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 309 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 309 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 309 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 309 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 309 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 309 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 309 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 309 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP B 309 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP B 309 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP B 309 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 309 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 309 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 309 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 355 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 237 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 238 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " 0.018 5.00e-02 4.00e+02 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1089 2.17 - 2.78: 54546 2.78 - 3.39: 78050 3.39 - 3.99: 102061 3.99 - 4.60: 160549 Nonbonded interactions: 396295 Sorted by model distance: nonbonded pdb=" OE1 GLU A 427 " pdb=" H GLU A 427 " model vdw 1.565 2.450 nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.584 2.450 nonbonded pdb=" O THR C 235 " pdb=" H GLN C 242 " model vdw 1.606 2.450 nonbonded pdb=" OD2 ASP B 522 " pdb=" HH TYR B 559 " model vdw 1.625 2.450 nonbonded pdb=" O VAL B 113 " pdb=" HG1 THR B 117 " model vdw 1.653 2.450 ... (remaining 396290 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.030 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 0.051 14784 Z= 0.152 Angle : 0.566 5.663 19914 Z= 0.337 Chirality : 0.037 0.137 2172 Planarity : 0.003 0.045 2565 Dihedral : 13.915 88.800 5667 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.07 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.13 (0.20), residues: 1775 helix: 1.27 (0.19), residues: 884 sheet: -1.32 (0.41), residues: 154 loop : -1.50 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 192 TYR 0.012 0.001 TYR B 620 PHE 0.009 0.001 PHE A 658 TRP 0.041 0.001 TRP B 309 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00317 (14784) covalent geometry : angle 0.56609 (19914) hydrogen bonds : bond 0.14899 ( 725) hydrogen bonds : angle 5.81903 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7650 (t0) cc_final: 0.7133 (t70) REVERT: A 347 ASP cc_start: 0.7821 (m-30) cc_final: 0.7529 (m-30) REVERT: A 441 MET cc_start: 0.8769 (ttm) cc_final: 0.8489 (ttm) REVERT: A 477 MET cc_start: 0.8164 (mtp) cc_final: 0.7678 (mtm) REVERT: B 27 ASP cc_start: 0.7736 (m-30) cc_final: 0.7467 (m-30) REVERT: B 356 MET cc_start: 0.7935 (ttt) cc_final: 0.7443 (ttt) REVERT: B 711 ILE cc_start: 0.8282 (pt) cc_final: 0.7678 (mt) REVERT: C 28 MET cc_start: 0.6323 (tmm) cc_final: 0.6027 (tmm) REVERT: D 65 TRP cc_start: 0.7097 (m-10) cc_final: 0.6703 (m100) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 1.3637 time to fit residues: 421.0578 Evaluate side-chains 228 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 292 ASN C 182 GLN C 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103094 restraints weight = 53971.824| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.30 r_work: 0.3205 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14784 Z= 0.136 Angle : 0.515 4.915 19914 Z= 0.273 Chirality : 0.037 0.143 2172 Planarity : 0.004 0.050 2565 Dihedral : 4.019 18.977 1957 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.96 % Favored : 94.93 % Rotamer: Outliers : 1.06 % Allowed : 8.86 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.08 (0.20), residues: 1775 helix: 1.51 (0.18), residues: 879 sheet: -1.42 (0.40), residues: 158 loop : -1.42 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 6 TYR 0.012 0.001 TYR D 41 PHE 0.013 0.001 PHE A 35 TRP 0.014 0.001 TRP B 309 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00309 (14784) covalent geometry : angle 0.51547 (19914) hydrogen bonds : bond 0.04443 ( 725) hydrogen bonds : angle 4.71565 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: A 160 ASP cc_start: 0.7795 (t0) cc_final: 0.7404 (t70) REVERT: A 294 ASP cc_start: 0.7691 (m-30) cc_final: 0.7221 (p0) REVERT: A 347 ASP cc_start: 0.8027 (m-30) cc_final: 0.7646 (m-30) REVERT: A 441 MET cc_start: 0.8997 (ttm) cc_final: 0.8773 (ttm) REVERT: A 477 MET cc_start: 0.8615 (mtp) cc_final: 0.8315 (mtm) REVERT: A 579 MET cc_start: 0.9043 (mtp) cc_final: 0.8688 (mtp) REVERT: A 692 GLU cc_start: 0.8354 (pt0) cc_final: 0.8076 (pt0) REVERT: B 27 ASP cc_start: 0.8548 (m-30) cc_final: 0.8225 (m-30) REVERT: B 356 MET cc_start: 0.8099 (ttt) cc_final: 0.7399 (ttt) REVERT: B 744 MET cc_start: 0.7177 (mmm) cc_final: 0.6949 (mmm) REVERT: B 754 ARG cc_start: 0.6490 (ttp80) cc_final: 0.6189 (ttt90) REVERT: C 66 MET cc_start: 0.8466 (mtp) cc_final: 0.8236 (mtt) REVERT: C 136 ARG cc_start: 0.8051 (ptp-110) cc_final: 0.7738 (ptp-170) REVERT: D 65 TRP cc_start: 0.7070 (m-10) cc_final: 0.6425 (m-10) REVERT: D 80 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8505 (mp) outliers start: 17 outliers final: 6 residues processed: 244 average time/residue: 1.3274 time to fit residues: 354.2752 Evaluate side-chains 225 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 167 optimal weight: 0.0000 chunk 46 optimal weight: 1.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN B 690 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102684 restraints weight = 54486.921| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.35 r_work: 0.3192 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14784 Z= 0.146 Angle : 0.501 4.801 19914 Z= 0.263 Chirality : 0.037 0.139 2172 Planarity : 0.004 0.062 2565 Dihedral : 4.008 18.803 1957 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 1.31 % Allowed : 10.30 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.21 (0.20), residues: 1775 helix: 1.63 (0.18), residues: 877 sheet: -1.35 (0.40), residues: 158 loop : -1.38 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 6 TYR 0.014 0.001 TYR D 41 PHE 0.010 0.001 PHE A 658 TRP 0.008 0.001 TRP B 309 HIS 0.007 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00342 (14784) covalent geometry : angle 0.50091 (19914) hydrogen bonds : bond 0.04064 ( 725) hydrogen bonds : angle 4.51457 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: A 160 ASP cc_start: 0.7748 (t0) cc_final: 0.7416 (t70) REVERT: A 294 ASP cc_start: 0.7546 (m-30) cc_final: 0.7155 (p0) REVERT: A 347 ASP cc_start: 0.8089 (m-30) cc_final: 0.7665 (m-30) REVERT: A 441 MET cc_start: 0.9019 (ttm) cc_final: 0.8806 (ttm) REVERT: A 477 MET cc_start: 0.8617 (mtp) cc_final: 0.8342 (mtm) REVERT: A 692 GLU cc_start: 0.8319 (pt0) cc_final: 0.7983 (pt0) REVERT: B 27 ASP cc_start: 0.8566 (m-30) cc_final: 0.8241 (m-30) REVERT: B 356 MET cc_start: 0.8079 (ttt) cc_final: 0.7448 (ttt) REVERT: B 697 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6562 (tt0) REVERT: B 744 MET cc_start: 0.7191 (mmm) cc_final: 0.6893 (mmm) REVERT: B 754 ARG cc_start: 0.6668 (ttp80) cc_final: 0.6362 (ttt90) REVERT: C 47 MET cc_start: 0.8725 (tpt) cc_final: 0.8515 (tpp) REVERT: C 64 MET cc_start: 0.8435 (mtt) cc_final: 0.8167 (mtt) REVERT: C 66 MET cc_start: 0.8470 (mtp) cc_final: 0.8212 (mtt) REVERT: C 216 ARG cc_start: 0.6841 (ptt180) cc_final: 0.6347 (ptp90) REVERT: D 80 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8492 (mp) outliers start: 21 outliers final: 9 residues processed: 226 average time/residue: 1.2993 time to fit residues: 321.6249 Evaluate side-chains 223 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 153 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN B 292 ASN B 690 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102468 restraints weight = 54203.153| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.34 r_work: 0.3188 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14784 Z= 0.145 Angle : 0.497 5.595 19914 Z= 0.261 Chirality : 0.037 0.139 2172 Planarity : 0.004 0.071 2565 Dihedral : 3.982 18.655 1957 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 1.31 % Allowed : 10.86 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.27 (0.20), residues: 1775 helix: 1.67 (0.18), residues: 880 sheet: -1.23 (0.40), residues: 156 loop : -1.38 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 6 TYR 0.015 0.001 TYR D 41 PHE 0.012 0.001 PHE D 118 TRP 0.024 0.001 TRP D 65 HIS 0.005 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00341 (14784) covalent geometry : angle 0.49707 (19914) hydrogen bonds : bond 0.03831 ( 725) hydrogen bonds : angle 4.41466 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7590 (t0) cc_final: 0.7251 (t70) REVERT: A 294 ASP cc_start: 0.7587 (m-30) cc_final: 0.7156 (p0) REVERT: A 347 ASP cc_start: 0.8132 (m-30) cc_final: 0.7702 (m-30) REVERT: A 441 MET cc_start: 0.9024 (ttm) cc_final: 0.8810 (ttm) REVERT: A 477 MET cc_start: 0.8655 (mtp) cc_final: 0.8364 (mtm) REVERT: A 579 MET cc_start: 0.9089 (mtp) cc_final: 0.8731 (mtp) REVERT: A 692 GLU cc_start: 0.8311 (pt0) cc_final: 0.7722 (tm-30) REVERT: B 1 MET cc_start: 0.7901 (ptt) cc_final: 0.7539 (ptt) REVERT: B 27 ASP cc_start: 0.8569 (m-30) cc_final: 0.8251 (m-30) REVERT: B 172 GLU cc_start: 0.8382 (tt0) cc_final: 0.7788 (tm-30) REVERT: B 688 MET cc_start: 0.8481 (ptt) cc_final: 0.8096 (ptm) REVERT: B 697 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6577 (tt0) REVERT: B 744 MET cc_start: 0.7115 (mmm) cc_final: 0.6720 (mmm) REVERT: B 754 ARG cc_start: 0.6588 (ttp80) cc_final: 0.6288 (ttt90) REVERT: C 66 MET cc_start: 0.8476 (mtp) cc_final: 0.8168 (mtt) REVERT: C 216 ARG cc_start: 0.6819 (ptt180) cc_final: 0.6311 (ptp90) REVERT: D 65 TRP cc_start: 0.6716 (m100) cc_final: 0.6110 (m100) REVERT: D 80 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8497 (mp) outliers start: 21 outliers final: 10 residues processed: 227 average time/residue: 1.3874 time to fit residues: 345.0331 Evaluate side-chains 219 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 9 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN B 690 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101785 restraints weight = 54131.474| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.23 r_work: 0.3183 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14784 Z= 0.172 Angle : 0.509 5.406 19914 Z= 0.267 Chirality : 0.038 0.140 2172 Planarity : 0.004 0.080 2565 Dihedral : 4.019 18.870 1957 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.18 % Favored : 94.70 % Rotamer: Outliers : 1.12 % Allowed : 11.86 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.24 (0.20), residues: 1775 helix: 1.66 (0.18), residues: 880 sheet: -1.24 (0.41), residues: 156 loop : -1.40 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 6 TYR 0.015 0.001 TYR D 41 PHE 0.014 0.001 PHE D 118 TRP 0.010 0.001 TRP A 406 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00409 (14784) covalent geometry : angle 0.50910 (19914) hydrogen bonds : bond 0.03902 ( 725) hydrogen bonds : angle 4.38738 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7269 (mp0) cc_final: 0.7049 (mp0) REVERT: A 160 ASP cc_start: 0.7562 (t0) cc_final: 0.7227 (t70) REVERT: A 347 ASP cc_start: 0.8080 (m-30) cc_final: 0.7581 (m-30) REVERT: A 441 MET cc_start: 0.9027 (ttm) cc_final: 0.8810 (ttm) REVERT: A 477 MET cc_start: 0.8672 (mtp) cc_final: 0.8378 (mtm) REVERT: A 692 GLU cc_start: 0.8323 (pt0) cc_final: 0.7750 (tm-30) REVERT: B 27 ASP cc_start: 0.8541 (m-30) cc_final: 0.8240 (m-30) REVERT: B 172 GLU cc_start: 0.8360 (tt0) cc_final: 0.7789 (tm-30) REVERT: B 697 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6591 (tt0) REVERT: B 744 MET cc_start: 0.7003 (mmm) cc_final: 0.6565 (mmm) REVERT: C 64 MET cc_start: 0.8595 (mtt) cc_final: 0.8143 (mtt) REVERT: C 191 GLU cc_start: 0.7211 (tp30) cc_final: 0.6925 (tt0) REVERT: C 216 ARG cc_start: 0.6834 (ptt180) cc_final: 0.6328 (ptp90) REVERT: D 65 TRP cc_start: 0.6738 (m-10) cc_final: 0.5930 (m100) outliers start: 18 outliers final: 13 residues processed: 224 average time/residue: 1.2859 time to fit residues: 316.2333 Evaluate side-chains 225 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 167 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN C 160 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100566 restraints weight = 54698.485| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.28 r_work: 0.3161 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14784 Z= 0.212 Angle : 0.531 5.005 19914 Z= 0.280 Chirality : 0.039 0.143 2172 Planarity : 0.004 0.094 2565 Dihedral : 4.114 19.379 1957 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.31 % Rotamer: Outliers : 1.37 % Allowed : 12.17 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.08 (0.20), residues: 1775 helix: 1.48 (0.18), residues: 888 sheet: -1.29 (0.40), residues: 156 loop : -1.46 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 6 TYR 0.015 0.001 TYR D 41 PHE 0.013 0.001 PHE A 520 TRP 0.012 0.001 TRP A 406 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00504 (14784) covalent geometry : angle 0.53129 (19914) hydrogen bonds : bond 0.04078 ( 725) hydrogen bonds : angle 4.42746 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7569 (t0) cc_final: 0.7232 (t70) REVERT: A 347 ASP cc_start: 0.7954 (m-30) cc_final: 0.7524 (m-30) REVERT: A 441 MET cc_start: 0.9068 (ttm) cc_final: 0.8858 (ttm) REVERT: A 477 MET cc_start: 0.8671 (mtp) cc_final: 0.8392 (mtm) REVERT: A 579 MET cc_start: 0.9162 (mtp) cc_final: 0.8917 (mtp) REVERT: A 692 GLU cc_start: 0.8431 (pt0) cc_final: 0.7834 (tm-30) REVERT: B 27 ASP cc_start: 0.8532 (m-30) cc_final: 0.8220 (m-30) REVERT: B 172 GLU cc_start: 0.8393 (tt0) cc_final: 0.7852 (tm-30) REVERT: B 697 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6548 (tt0) REVERT: B 716 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8012 (mm-30) REVERT: B 744 MET cc_start: 0.7110 (mmm) cc_final: 0.6684 (mmm) REVERT: C 216 ARG cc_start: 0.6879 (ptt180) cc_final: 0.6370 (ptp90) REVERT: D 65 TRP cc_start: 0.6716 (m-10) cc_final: 0.5949 (m100) outliers start: 22 outliers final: 15 residues processed: 229 average time/residue: 1.4417 time to fit residues: 361.1851 Evaluate side-chains 229 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 26 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 14 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.102090 restraints weight = 54082.113| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.35 r_work: 0.3185 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14784 Z= 0.113 Angle : 0.490 6.025 19914 Z= 0.256 Chirality : 0.037 0.142 2172 Planarity : 0.004 0.092 2565 Dihedral : 3.995 19.948 1957 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 1.00 % Allowed : 12.98 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.33 (0.20), residues: 1775 helix: 1.69 (0.18), residues: 890 sheet: -1.22 (0.41), residues: 156 loop : -1.35 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 6 TYR 0.016 0.001 TYR D 41 PHE 0.010 0.001 PHE A 658 TRP 0.009 0.001 TRP A 406 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00265 (14784) covalent geometry : angle 0.49026 (19914) hydrogen bonds : bond 0.03650 ( 725) hydrogen bonds : angle 4.27770 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7491 (t0) cc_final: 0.7171 (t70) REVERT: A 347 ASP cc_start: 0.7935 (m-30) cc_final: 0.7497 (m-30) REVERT: A 441 MET cc_start: 0.9032 (ttm) cc_final: 0.8826 (ttm) REVERT: A 477 MET cc_start: 0.8624 (mtp) cc_final: 0.8332 (mtm) REVERT: A 692 GLU cc_start: 0.8356 (pt0) cc_final: 0.7827 (tm-30) REVERT: B 27 ASP cc_start: 0.8525 (m-30) cc_final: 0.8205 (m-30) REVERT: B 172 GLU cc_start: 0.8375 (tt0) cc_final: 0.7803 (tm-30) REVERT: B 688 MET cc_start: 0.8470 (ptt) cc_final: 0.8007 (ptm) REVERT: B 697 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6443 (tt0) REVERT: B 716 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7970 (mm-30) REVERT: B 744 MET cc_start: 0.6978 (mmm) cc_final: 0.6569 (mmm) REVERT: C 64 MET cc_start: 0.8640 (mtt) cc_final: 0.8206 (mtt) REVERT: C 191 GLU cc_start: 0.7181 (tp30) cc_final: 0.6913 (tt0) REVERT: C 216 ARG cc_start: 0.6841 (ptt180) cc_final: 0.6344 (ptp90) outliers start: 16 outliers final: 11 residues processed: 223 average time/residue: 1.4818 time to fit residues: 360.8415 Evaluate side-chains 225 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 16 optimal weight: 6.9990 chunk 67 optimal weight: 0.0980 chunk 81 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.141273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103047 restraints weight = 54370.808| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.28 r_work: 0.3180 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14784 Z= 0.150 Angle : 0.504 5.590 19914 Z= 0.262 Chirality : 0.037 0.141 2172 Planarity : 0.004 0.096 2565 Dihedral : 3.997 20.508 1957 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 1.31 % Allowed : 13.17 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.31 (0.20), residues: 1775 helix: 1.67 (0.18), residues: 891 sheet: -1.22 (0.41), residues: 156 loop : -1.36 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 6 TYR 0.017 0.001 TYR D 41 PHE 0.010 0.001 PHE A 520 TRP 0.010 0.001 TRP D 65 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00357 (14784) covalent geometry : angle 0.50369 (19914) hydrogen bonds : bond 0.03714 ( 725) hydrogen bonds : angle 4.27425 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7602 (t0) cc_final: 0.7272 (t70) REVERT: A 347 ASP cc_start: 0.7909 (m-30) cc_final: 0.7496 (m-30) REVERT: A 441 MET cc_start: 0.9067 (ttm) cc_final: 0.8860 (ttm) REVERT: A 477 MET cc_start: 0.8622 (mtp) cc_final: 0.8349 (mtm) REVERT: A 692 GLU cc_start: 0.8360 (pt0) cc_final: 0.7870 (tm-30) REVERT: B 27 ASP cc_start: 0.8646 (m-30) cc_final: 0.8364 (m-30) REVERT: B 172 GLU cc_start: 0.8386 (tt0) cc_final: 0.7848 (tm-30) REVERT: B 697 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6508 (tt0) REVERT: B 716 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7997 (mm-30) REVERT: B 744 MET cc_start: 0.7069 (mmm) cc_final: 0.6646 (mmm) REVERT: C 216 ARG cc_start: 0.6866 (ptt180) cc_final: 0.6362 (ptp90) REVERT: D 77 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6450 (ttt-90) REVERT: D 80 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8668 (mp) outliers start: 21 outliers final: 15 residues processed: 225 average time/residue: 1.3221 time to fit residues: 326.2058 Evaluate side-chains 234 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102779 restraints weight = 54057.722| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.36 r_work: 0.3196 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14784 Z= 0.104 Angle : 0.485 6.260 19914 Z= 0.251 Chirality : 0.036 0.138 2172 Planarity : 0.004 0.101 2565 Dihedral : 3.888 20.142 1957 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 1.25 % Allowed : 13.36 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.47 (0.21), residues: 1775 helix: 1.82 (0.18), residues: 892 sheet: -1.11 (0.42), residues: 156 loop : -1.30 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 6 TYR 0.018 0.001 TYR D 41 PHE 0.009 0.001 PHE B 740 TRP 0.016 0.001 TRP D 65 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00244 (14784) covalent geometry : angle 0.48466 (19914) hydrogen bonds : bond 0.03456 ( 725) hydrogen bonds : angle 4.16725 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7579 (t0) cc_final: 0.7263 (t70) REVERT: A 168 ARG cc_start: 0.7139 (mtm110) cc_final: 0.6800 (mtm-85) REVERT: A 347 ASP cc_start: 0.8088 (m-30) cc_final: 0.7664 (m-30) REVERT: A 441 MET cc_start: 0.9025 (ttm) cc_final: 0.8820 (ttm) REVERT: A 477 MET cc_start: 0.8568 (mtp) cc_final: 0.8286 (mtm) REVERT: A 692 GLU cc_start: 0.8328 (pt0) cc_final: 0.7865 (tm-30) REVERT: B 27 ASP cc_start: 0.8639 (m-30) cc_final: 0.8345 (m-30) REVERT: B 172 GLU cc_start: 0.8351 (tt0) cc_final: 0.7794 (tm-30) REVERT: B 697 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6237 (tt0) REVERT: B 716 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: B 744 MET cc_start: 0.6975 (mmm) cc_final: 0.6611 (mmm) REVERT: C 64 MET cc_start: 0.8620 (mtt) cc_final: 0.8189 (mtt) REVERT: C 191 GLU cc_start: 0.7215 (tp30) cc_final: 0.6920 (tt0) REVERT: C 216 ARG cc_start: 0.6840 (ptt180) cc_final: 0.6340 (ptp90) REVERT: D 77 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6351 (ttt-90) REVERT: D 80 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8630 (mp) outliers start: 20 outliers final: 12 residues processed: 228 average time/residue: 1.3149 time to fit residues: 328.3346 Evaluate side-chains 230 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 70 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 GLN C 194 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101921 restraints weight = 54072.042| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.31 r_work: 0.3180 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14784 Z= 0.155 Angle : 0.507 5.786 19914 Z= 0.264 Chirality : 0.037 0.140 2172 Planarity : 0.004 0.106 2565 Dihedral : 3.922 20.566 1957 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.85 % Favored : 95.04 % Rotamer: Outliers : 1.25 % Allowed : 13.48 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.41 (0.21), residues: 1775 helix: 1.80 (0.18), residues: 885 sheet: -1.17 (0.42), residues: 156 loop : -1.34 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 6 TYR 0.017 0.001 TYR D 41 PHE 0.010 0.001 PHE A 520 TRP 0.014 0.001 TRP D 65 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00372 (14784) covalent geometry : angle 0.50741 (19914) hydrogen bonds : bond 0.03657 ( 725) hydrogen bonds : angle 4.21024 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7579 (t0) cc_final: 0.7257 (t70) REVERT: A 168 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6842 (mtm-85) REVERT: A 347 ASP cc_start: 0.8105 (m-30) cc_final: 0.7612 (m-30) REVERT: A 441 MET cc_start: 0.9038 (ttm) cc_final: 0.8828 (ttm) REVERT: A 477 MET cc_start: 0.8594 (mtp) cc_final: 0.8324 (mtm) REVERT: A 692 GLU cc_start: 0.8351 (pt0) cc_final: 0.7868 (tm-30) REVERT: B 1 MET cc_start: 0.8017 (ptt) cc_final: 0.7693 (ptt) REVERT: B 27 ASP cc_start: 0.8665 (m-30) cc_final: 0.8369 (m-30) REVERT: B 172 GLU cc_start: 0.8370 (tt0) cc_final: 0.7829 (tm-30) REVERT: B 697 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6287 (tt0) REVERT: B 716 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: B 744 MET cc_start: 0.7035 (mmm) cc_final: 0.6664 (mmm) REVERT: C 191 GLU cc_start: 0.7279 (tp30) cc_final: 0.7009 (tt0) REVERT: C 216 ARG cc_start: 0.6914 (ptt180) cc_final: 0.6416 (ptp90) REVERT: D 77 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6443 (ttt-90) outliers start: 20 outliers final: 15 residues processed: 226 average time/residue: 1.4684 time to fit residues: 364.4637 Evaluate side-chains 234 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 77 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 134 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.141749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104576 restraints weight = 53986.955| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.13 r_work: 0.3197 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14784 Z= 0.122 Angle : 0.493 6.022 19914 Z= 0.256 Chirality : 0.037 0.138 2172 Planarity : 0.004 0.107 2565 Dihedral : 3.881 19.880 1957 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 1.06 % Allowed : 13.73 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.46 (0.21), residues: 1775 helix: 1.85 (0.18), residues: 887 sheet: -1.17 (0.44), residues: 146 loop : -1.34 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 6 TYR 0.017 0.001 TYR D 41 PHE 0.009 0.001 PHE A 658 TRP 0.020 0.001 TRP D 65 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00289 (14784) covalent geometry : angle 0.49277 (19914) hydrogen bonds : bond 0.03525 ( 725) hydrogen bonds : angle 4.16381 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10356.41 seconds wall clock time: 175 minutes 37.53 seconds (10537.53 seconds total)