Starting phenix.real_space_refine on Wed Mar 4 13:46:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qd8_13910/03_2026/7qd8_13910.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qd8_13910/03_2026/7qd8_13910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qd8_13910/03_2026/7qd8_13910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qd8_13910/03_2026/7qd8_13910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qd8_13910/03_2026/7qd8_13910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qd8_13910/03_2026/7qd8_13910.map" } resolution = 3.6 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= 0.003 sd= 0.152 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8996 2.51 5 N 2458 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 7043 Classifications: {'peptide': 865} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 839} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 7043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 7043 Classifications: {'peptide': 865} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 839} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 3.12, per 1000 atoms: 0.22 Number of scatterers: 14086 At special positions: 0 Unit cell: (164.852, 113.636, 113.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2590 8.00 N 2458 7.00 C 8996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.20 Conformation dependent library (CDL) restraints added in 448.2 milliseconds 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 5 sheets defined 73.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.896A pdb=" N GLU A 23 " --> pdb=" O ARG A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.660A pdb=" N HIS A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.511A pdb=" N GLU A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 69 " --> pdb=" O LEU A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.952A pdb=" N PHE A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 112 Processing helix chain 'A' and resid 118 through 136 removed outlier: 4.145A pdb=" N GLN A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP A 135 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.510A pdb=" N MET A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 184 removed outlier: 3.840A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.543A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.707A pdb=" N ASP A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.069A pdb=" N ARG A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 269 through 319 removed outlier: 3.952A pdb=" N SER A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.624A pdb=" N LYS A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.632A pdb=" N VAL A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.799A pdb=" N ASN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.790A pdb=" N VAL A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 398 removed outlier: 3.547A pdb=" N LEU A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.925A pdb=" N GLU A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.676A pdb=" N LEU A 459 " --> pdb=" O HIS A 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.853A pdb=" N TYR A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 489' Processing helix chain 'A' and resid 491 through 499 removed outlier: 5.233A pdb=" N GLU A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 530 removed outlier: 3.868A pdb=" N TYR A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 4.200A pdb=" N ALA A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 586 Processing helix chain 'A' and resid 587 through 592 removed outlier: 3.504A pdb=" N GLN A 591 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 618 removed outlier: 3.690A pdb=" N ASN A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 641 removed outlier: 3.968A pdb=" N MET A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 664 Processing helix chain 'A' and resid 665 through 670 removed outlier: 4.020A pdb=" N SER A 668 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 737 removed outlier: 4.544A pdb=" N LEU A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS A 731 " --> pdb=" O ARG A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 766 removed outlier: 4.288A pdb=" N THR A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 808 removed outlier: 3.526A pdb=" N ILE A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 812 removed outlier: 3.788A pdb=" N GLU A 812 " --> pdb=" O GLU A 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 812' Processing helix chain 'A' and resid 813 through 824 Processing helix chain 'A' and resid 827 through 838 Processing helix chain 'A' and resid 841 through 866 removed outlier: 3.661A pdb=" N MET A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A 854 " --> pdb=" O GLU A 850 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 855 " --> pdb=" O MET A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 891 removed outlier: 3.665A pdb=" N GLN A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 removed outlier: 4.391A pdb=" N GLU A 900 " --> pdb=" O GLY A 896 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 901 " --> pdb=" O GLU A 897 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 909 " --> pdb=" O ASP A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 938 removed outlier: 3.547A pdb=" N ILE A 916 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 929 " --> pdb=" O THR A 925 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 930 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.914A pdb=" N GLU B 23 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.640A pdb=" N HIS B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.510A pdb=" N GLU B 68 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 69 " --> pdb=" O LEU B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 69' Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.970A pdb=" N PHE B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 112 Processing helix chain 'B' and resid 118 through 136 removed outlier: 4.123A pdb=" N GLN B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.534A pdb=" N MET B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 184 removed outlier: 3.765A pdb=" N ILE B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 176 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.535A pdb=" N ALA B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.707A pdb=" N ASP B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 removed outlier: 4.006A pdb=" N ARG B 229 " --> pdb=" O LYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 269 through 313 removed outlier: 3.874A pdb=" N SER B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 321 through 343 removed outlier: 3.618A pdb=" N LYS B 325 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 329 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 356 through 370 removed outlier: 3.645A pdb=" N VAL B 360 " --> pdb=" O TRP B 356 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 390 removed outlier: 3.934A pdb=" N ASN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TYR B 387 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 398 Processing helix chain 'B' and resid 407 through 424 removed outlier: 3.813A pdb=" N GLU B 422 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 471 removed outlier: 3.516A pdb=" N LEU B 459 " --> pdb=" O HIS B 455 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 461 " --> pdb=" O TYR B 457 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B 470 " --> pdb=" O ARG B 466 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.635A pdb=" N TYR B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 484 through 489' Processing helix chain 'B' and resid 491 through 499 removed outlier: 5.178A pdb=" N GLU B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 530 removed outlier: 3.825A pdb=" N TYR B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 570 removed outlier: 4.181A pdb=" N ALA B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 586 Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 602 through 618 removed outlier: 3.793A pdb=" N ASN B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.691A pdb=" N THR B 629 " --> pdb=" O MET B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 641 removed outlier: 4.003A pdb=" N MET B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 664 removed outlier: 3.627A pdb=" N ASN B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 664 " --> pdb=" O PHE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 4.030A pdb=" N SER B 668 " --> pdb=" O LYS B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 737 removed outlier: 4.670A pdb=" N LEU B 730 " --> pdb=" O ALA B 726 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N HIS B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 766 removed outlier: 4.462A pdb=" N THR B 756 " --> pdb=" O THR B 752 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 808 removed outlier: 3.521A pdb=" N ILE B 807 " --> pdb=" O ASN B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 812 removed outlier: 3.845A pdb=" N GLU B 812 " --> pdb=" O GLU B 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 809 through 812' Processing helix chain 'B' and resid 813 through 824 Processing helix chain 'B' and resid 827 through 838 Processing helix chain 'B' and resid 841 through 866 removed outlier: 3.712A pdb=" N MET B 851 " --> pdb=" O ALA B 847 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 854 " --> pdb=" O GLU B 850 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 855 " --> pdb=" O MET B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 891 removed outlier: 3.637A pdb=" N GLN B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 907 removed outlier: 4.477A pdb=" N GLU B 900 " --> pdb=" O GLY B 896 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 901 " --> pdb=" O GLU B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 938 removed outlier: 3.783A pdb=" N GLU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 930 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 933 " --> pdb=" O GLU B 929 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 403 Processing sheet with id=AA2, first strand: chain 'A' and resid 573 through 574 removed outlier: 7.632A pdb=" N ILE A 573 " --> pdb=" O ASN A 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 720 through 722 removed outlier: 6.524A pdb=" N LYS A 720 " --> pdb=" O ARG A 769 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 573 through 574 removed outlier: 7.649A pdb=" N ILE B 573 " --> pdb=" O ASN B 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 720 through 722 removed outlier: 6.561A pdb=" N LYS B 720 " --> pdb=" O ARG B 769 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 758 hydrogen bonds defined for protein. 2235 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: 1.65 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4622 1.34 - 1.46: 2806 1.46 - 1.58: 6860 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 14370 Sorted by residual: bond pdb=" CB GLN B 188 " pdb=" CG GLN B 188 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" C TYR A 61 " pdb=" N PRO A 62 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 bond pdb=" C TYR B 61 " pdb=" N PRO B 62 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.48e+00 bond pdb=" CA GLY B 939 " pdb=" C GLY B 939 " ideal model delta sigma weight residual 1.510 1.528 -0.018 1.46e-02 4.69e+03 1.48e+00 bond pdb=" CA GLY A 939 " pdb=" C GLY A 939 " ideal model delta sigma weight residual 1.510 1.527 -0.018 1.46e-02 4.69e+03 1.45e+00 ... (remaining 14365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 18775 1.76 - 3.52: 509 3.52 - 5.28: 96 5.28 - 7.04: 26 7.04 - 8.80: 14 Bond angle restraints: 19420 Sorted by residual: angle pdb=" C ILE B 202 " pdb=" N ASN B 203 " pdb=" CA ASN B 203 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.09e+01 angle pdb=" N ILE B 59 " pdb=" CA ILE B 59 " pdb=" C ILE B 59 " ideal model delta sigma weight residual 112.96 108.42 4.54 1.00e+00 1.00e+00 2.06e+01 angle pdb=" CA ARG B 384 " pdb=" CB ARG B 384 " pdb=" CG ARG B 384 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 angle pdb=" C ILE A 202 " pdb=" N ASN A 203 " pdb=" CA ASN A 203 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 angle pdb=" CA LYS B 564 " pdb=" CB LYS B 564 " pdb=" CG LYS B 564 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 ... (remaining 19415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7753 17.91 - 35.82: 755 35.82 - 53.72: 119 53.72 - 71.63: 28 71.63 - 89.54: 11 Dihedral angle restraints: 8666 sinusoidal: 3580 harmonic: 5086 Sorted by residual: dihedral pdb=" CA VAL A 360 " pdb=" C VAL A 360 " pdb=" N GLU A 361 " pdb=" CA GLU A 361 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU B 458 " pdb=" CG GLU B 458 " pdb=" CD GLU B 458 " pdb=" OE1 GLU B 458 " ideal model delta sinusoidal sigma weight residual 0.00 -88.84 88.84 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA GLU A 358 " pdb=" C GLU A 358 " pdb=" N MET A 359 " pdb=" CA MET A 359 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 8663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1668 0.052 - 0.105: 410 0.105 - 0.157: 68 0.157 - 0.209: 10 0.209 - 0.261: 2 Chirality restraints: 2158 Sorted by residual: chirality pdb=" CB THR A 750 " pdb=" CA THR A 750 " pdb=" OG1 THR A 750 " pdb=" CG2 THR A 750 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB THR B 750 " pdb=" CA THR B 750 " pdb=" OG1 THR B 750 " pdb=" CG2 THR B 750 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA GLU B 283 " pdb=" N GLU B 283 " pdb=" C GLU B 283 " pdb=" CB GLU B 283 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2155 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 501 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO B 502 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 501 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A 502 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 891 " -0.021 2.00e-02 2.50e+03 1.74e-02 5.29e+00 pdb=" CG PHE B 891 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 891 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 891 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 891 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 891 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 891 " -0.003 2.00e-02 2.50e+03 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3628 2.80 - 3.32: 13263 3.32 - 3.85: 22903 3.85 - 4.37: 26257 4.37 - 4.90: 44035 Nonbonded interactions: 110086 Sorted by model distance: nonbonded pdb=" O TYR A 819 " pdb=" OG1 THR A 823 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR A 385 " pdb=" OE2 GLU A 458 " model vdw 2.278 3.040 nonbonded pdb=" O HIS B 481 " pdb=" OH TYR B 488 " model vdw 2.283 3.040 nonbonded pdb=" O HIS A 481 " pdb=" OH TYR A 488 " model vdw 2.319 3.040 nonbonded pdb=" O TYR A 391 " pdb=" OG1 THR A 394 " model vdw 2.329 3.040 ... (remaining 110081 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.710 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 12.350 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14370 Z= 0.179 Angle : 0.745 8.805 19420 Z= 0.393 Chirality : 0.047 0.261 2158 Planarity : 0.005 0.066 2476 Dihedral : 14.487 89.540 5374 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -1.83 (0.18), residues: 1706 helix: -1.15 (0.14), residues: 1128 sheet: None (None), residues: 0 loop : -0.98 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 389 TYR 0.027 0.002 TYR A 811 PHE 0.040 0.002 PHE B 891 TRP 0.008 0.001 TRP B 102 HIS 0.007 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00393 (14370) covalent geometry : angle 0.74485 (19420) hydrogen bonds : bond 0.15568 ( 758) hydrogen bonds : angle 5.84669 ( 2235) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7955 (tptp) cc_final: 0.7591 (tppt) REVERT: A 39 LEU cc_start: 0.8649 (mm) cc_final: 0.8439 (mm) REVERT: A 456 TYR cc_start: 0.5074 (m-10) cc_final: 0.4102 (t80) REVERT: B 274 TYR cc_start: 0.3873 (m-10) cc_final: 0.3536 (m-80) REVERT: B 819 TYR cc_start: 0.5661 (t80) cc_final: 0.5349 (t80) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0851 time to fit residues: 21.1929 Evaluate side-chains 127 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.0270 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 116 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN B 43 HIS B 83 GLN B 116 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.186691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.164108 restraints weight = 26795.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.163502 restraints weight = 31478.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.164953 restraints weight = 24625.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.165419 restraints weight = 18633.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.165566 restraints weight = 18180.752| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14370 Z= 0.118 Angle : 0.495 7.242 19420 Z= 0.262 Chirality : 0.038 0.141 2158 Planarity : 0.004 0.053 2476 Dihedral : 4.208 16.438 1898 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.60 % Allowed : 8.28 % Favored : 91.13 % 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: -0.67 (0.19), residues: 1706 helix: -0.12 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.87 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 384 TYR 0.015 0.001 TYR B 387 PHE 0.020 0.002 PHE A 329 TRP 0.006 0.001 TRP A 528 HIS 0.010 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00260 (14370) covalent geometry : angle 0.49540 (19420) hydrogen bonds : bond 0.04103 ( 758) hydrogen bonds : angle 4.00961 ( 2235) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 456 TYR cc_start: 0.5456 (m-10) cc_final: 0.4531 (t80) REVERT: B 625 MET cc_start: 0.6458 (tpt) cc_final: 0.6197 (tpt) outliers start: 9 outliers final: 1 residues processed: 141 average time/residue: 0.0919 time to fit residues: 21.4374 Evaluate side-chains 119 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 155 optimal weight: 4.9990 chunk 159 optimal weight: 0.0870 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 217 GLN B 296 HIS ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.186853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.164531 restraints weight = 26966.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.163058 restraints weight = 30490.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.164723 restraints weight = 25686.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.164791 restraints weight = 19430.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.164979 restraints weight = 17599.243| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14370 Z= 0.105 Angle : 0.482 7.914 19420 Z= 0.250 Chirality : 0.037 0.150 2158 Planarity : 0.003 0.047 2476 Dihedral : 3.994 15.240 1898 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.86 % Allowed : 11.26 % Favored : 87.88 % 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: -0.02 (0.20), residues: 1706 helix: 0.38 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -0.62 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.013 0.001 TYR A 819 PHE 0.013 0.001 PHE A 760 TRP 0.005 0.001 TRP B 923 HIS 0.011 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00231 (14370) covalent geometry : angle 0.48183 (19420) hydrogen bonds : bond 0.03735 ( 758) hydrogen bonds : angle 3.78906 ( 2235) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 456 TYR cc_start: 0.5429 (m-10) cc_final: 0.4520 (t80) REVERT: A 625 MET cc_start: 0.6682 (tpt) cc_final: 0.6455 (tpt) REVERT: A 891 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.5578 (m-10) REVERT: B 625 MET cc_start: 0.6756 (tpt) cc_final: 0.6474 (tpt) REVERT: B 819 TYR cc_start: 0.6036 (t80) cc_final: 0.5775 (t80) REVERT: B 891 PHE cc_start: 0.6794 (OUTLIER) cc_final: 0.5414 (m-10) outliers start: 13 outliers final: 9 residues processed: 138 average time/residue: 0.0837 time to fit residues: 19.5015 Evaluate side-chains 129 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** 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 = 0.4588 r_free = 0.4588 target = 0.181134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.157076 restraints weight = 26917.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.156637 restraints weight = 29875.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.158045 restraints weight = 23712.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.158105 restraints weight = 16743.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.158258 restraints weight = 15589.563| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14370 Z= 0.202 Angle : 0.596 11.633 19420 Z= 0.309 Chirality : 0.041 0.191 2158 Planarity : 0.004 0.044 2476 Dihedral : 4.474 18.702 1898 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.85 % Allowed : 12.78 % Favored : 85.36 % 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: -0.29 (0.20), residues: 1706 helix: 0.18 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -0.73 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 480 TYR 0.027 0.002 TYR A 819 PHE 0.023 0.002 PHE B 891 TRP 0.009 0.001 TRP A 528 HIS 0.007 0.001 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00475 (14370) covalent geometry : angle 0.59587 (19420) hydrogen bonds : bond 0.04521 ( 758) hydrogen bonds : angle 4.01661 ( 2235) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 456 TYR cc_start: 0.5655 (m-10) cc_final: 0.4540 (t80) REVERT: A 891 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.5852 (m-10) REVERT: B 891 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.5648 (m-10) outliers start: 28 outliers final: 13 residues processed: 153 average time/residue: 0.0842 time to fit residues: 21.3314 Evaluate side-chains 136 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 28 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 116 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN A 958 ASN B 83 GLN B 116 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.183765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.160381 restraints weight = 26756.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.160030 restraints weight = 33206.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.161421 restraints weight = 24728.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.161719 restraints weight = 18132.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.161802 restraints weight = 17700.095| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14370 Z= 0.118 Angle : 0.517 11.430 19420 Z= 0.262 Chirality : 0.037 0.155 2158 Planarity : 0.003 0.033 2476 Dihedral : 4.076 15.751 1898 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.99 % Allowed : 14.57 % Favored : 83.44 % 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: 0.05 (0.20), residues: 1706 helix: 0.45 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -0.65 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 390 TYR 0.026 0.001 TYR B 819 PHE 0.014 0.001 PHE B 891 TRP 0.006 0.001 TRP B 923 HIS 0.010 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00268 (14370) covalent geometry : angle 0.51703 (19420) hydrogen bonds : bond 0.03765 ( 758) hydrogen bonds : angle 3.72636 ( 2235) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 456 TYR cc_start: 0.5630 (m-10) cc_final: 0.4527 (t80) REVERT: A 891 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.5622 (m-10) REVERT: B 832 MET cc_start: 0.7136 (mmm) cc_final: 0.6897 (mmm) REVERT: B 891 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.5402 (m-10) outliers start: 30 outliers final: 20 residues processed: 153 average time/residue: 0.0926 time to fit residues: 23.1222 Evaluate side-chains 147 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 63 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN B 116 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 296 HIS ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.182977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.159012 restraints weight = 26652.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.158631 restraints weight = 30304.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.160317 restraints weight = 23914.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.160058 restraints weight = 17001.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.160135 restraints weight = 16949.727| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14370 Z= 0.155 Angle : 0.563 11.576 19420 Z= 0.286 Chirality : 0.039 0.161 2158 Planarity : 0.003 0.030 2476 Dihedral : 4.224 16.768 1898 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.32 % Allowed : 15.70 % Favored : 81.99 % 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: -0.03 (0.20), residues: 1706 helix: 0.43 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -0.77 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 480 TYR 0.021 0.002 TYR B 811 PHE 0.020 0.002 PHE B 891 TRP 0.007 0.001 TRP B 923 HIS 0.010 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00362 (14370) covalent geometry : angle 0.56284 (19420) hydrogen bonds : bond 0.04096 ( 758) hydrogen bonds : angle 3.80403 ( 2235) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 435 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.6511 (m-70) REVERT: A 456 TYR cc_start: 0.5663 (m-10) cc_final: 0.4524 (t80) REVERT: A 891 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.5635 (m-10) REVERT: B 295 ILE cc_start: 0.7063 (mm) cc_final: 0.6851 (mm) REVERT: B 891 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.5533 (m-10) outliers start: 35 outliers final: 24 residues processed: 149 average time/residue: 0.0893 time to fit residues: 21.7639 Evaluate side-chains 149 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 811 TYR Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 164 optimal weight: 0.2980 chunk 150 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** 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 = 0.4595 r_free = 0.4595 target = 0.181895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.157832 restraints weight = 26529.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.157423 restraints weight = 32261.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.159171 restraints weight = 23782.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.159038 restraints weight = 16842.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.159297 restraints weight = 15513.076| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14370 Z= 0.151 Angle : 0.555 12.096 19420 Z= 0.280 Chirality : 0.039 0.160 2158 Planarity : 0.003 0.036 2476 Dihedral : 4.201 16.904 1898 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.19 % Allowed : 16.49 % Favored : 81.32 % 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: -0.00 (0.20), residues: 1706 helix: 0.44 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -0.75 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 727 TYR 0.016 0.002 TYR A 819 PHE 0.024 0.002 PHE A 232 TRP 0.007 0.001 TRP B 923 HIS 0.008 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00351 (14370) covalent geometry : angle 0.55467 (19420) hydrogen bonds : bond 0.04027 ( 758) hydrogen bonds : angle 3.78286 ( 2235) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6476 (m-70) REVERT: A 456 TYR cc_start: 0.5248 (m-10) cc_final: 0.4028 (t80) REVERT: A 891 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.5656 (m-10) REVERT: B 425 LYS cc_start: 0.5590 (mmtt) cc_final: 0.5057 (pttm) REVERT: B 891 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.5501 (m-10) outliers start: 33 outliers final: 23 residues processed: 152 average time/residue: 0.0940 time to fit residues: 23.1167 Evaluate side-chains 151 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 155 optimal weight: 0.0270 chunk 131 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** 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 = 0.4605 r_free = 0.4605 target = 0.182543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.159492 restraints weight = 26528.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.158837 restraints weight = 31766.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.160655 restraints weight = 24997.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.160221 restraints weight = 17374.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.160669 restraints weight = 17239.528| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14370 Z= 0.150 Angle : 0.561 12.063 19420 Z= 0.282 Chirality : 0.039 0.164 2158 Planarity : 0.003 0.038 2476 Dihedral : 4.216 17.250 1898 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.58 % Allowed : 16.49 % Favored : 80.93 % 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: 0.01 (0.20), residues: 1706 helix: 0.48 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.80 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 255 TYR 0.017 0.002 TYR A 811 PHE 0.021 0.002 PHE A 232 TRP 0.007 0.001 TRP B 923 HIS 0.008 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00348 (14370) covalent geometry : angle 0.56063 (19420) hydrogen bonds : bond 0.04023 ( 758) hydrogen bonds : angle 3.78265 ( 2235) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6114 (pt0) REVERT: A 435 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6670 (m-70) REVERT: A 456 TYR cc_start: 0.5211 (m-10) cc_final: 0.4027 (t80) REVERT: A 819 TYR cc_start: 0.6527 (t80) cc_final: 0.6303 (t80) REVERT: A 891 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.5718 (m-10) REVERT: B 425 LYS cc_start: 0.5578 (mmtt) cc_final: 0.5021 (pttm) REVERT: B 435 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.5961 (m-70) REVERT: B 891 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.5499 (m-10) outliers start: 39 outliers final: 24 residues processed: 156 average time/residue: 0.0775 time to fit residues: 20.0045 Evaluate side-chains 158 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.183169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.159282 restraints weight = 26573.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.158919 restraints weight = 28903.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.160570 restraints weight = 21800.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.160337 restraints weight = 16686.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.160564 restraints weight = 14797.346| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14370 Z= 0.117 Angle : 0.532 11.938 19420 Z= 0.266 Chirality : 0.038 0.158 2158 Planarity : 0.003 0.041 2476 Dihedral : 4.023 16.147 1898 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.05 % Allowed : 17.42 % Favored : 80.53 % 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: 1706 helix: 0.65 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -0.70 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 255 TYR 0.013 0.001 TYR A 811 PHE 0.019 0.002 PHE A 232 TRP 0.008 0.001 TRP B 102 HIS 0.007 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00265 (14370) covalent geometry : angle 0.53196 (19420) hydrogen bonds : bond 0.03694 ( 758) hydrogen bonds : angle 3.68423 ( 2235) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6560 (pt0) REVERT: A 188 GLN cc_start: 0.6978 (tp40) cc_final: 0.6523 (tp-100) REVERT: A 435 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.6634 (m-70) REVERT: A 456 TYR cc_start: 0.5354 (m-10) cc_final: 0.4213 (t80) REVERT: A 891 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.5708 (m-10) REVERT: B 101 LEU cc_start: 0.8247 (tp) cc_final: 0.7991 (tt) REVERT: B 188 GLN cc_start: 0.6981 (tp40) cc_final: 0.6689 (tp-100) REVERT: B 425 LYS cc_start: 0.5451 (mmtt) cc_final: 0.4887 (pttm) REVERT: B 435 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6050 (m-70) REVERT: B 891 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.5375 (m-10) outliers start: 31 outliers final: 22 residues processed: 153 average time/residue: 0.0993 time to fit residues: 24.2216 Evaluate side-chains 152 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 141 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 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 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** 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 = 0.4626 r_free = 0.4626 target = 0.184624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.161755 restraints weight = 26473.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.161957 restraints weight = 29825.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.163349 restraints weight = 23243.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.163215 restraints weight = 16701.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.163245 restraints weight = 16837.508| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14370 Z= 0.112 Angle : 0.537 12.887 19420 Z= 0.267 Chirality : 0.037 0.156 2158 Planarity : 0.003 0.041 2476 Dihedral : 3.929 15.861 1898 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.05 % Allowed : 17.62 % Favored : 80.33 % 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: 0.39 (0.21), residues: 1706 helix: 0.78 (0.16), residues: 1144 sheet: None (None), residues: 0 loop : -0.67 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 255 TYR 0.013 0.001 TYR B 811 PHE 0.018 0.001 PHE A 232 TRP 0.008 0.001 TRP A 64 HIS 0.007 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00253 (14370) covalent geometry : angle 0.53680 (19420) hydrogen bonds : bond 0.03561 ( 758) hydrogen bonds : angle 3.64868 ( 2235) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6574 (pt0) REVERT: A 277 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7090 (mm) REVERT: A 435 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6686 (m-70) REVERT: A 456 TYR cc_start: 0.5372 (m-10) cc_final: 0.4213 (t80) REVERT: A 597 THR cc_start: 0.5687 (OUTLIER) cc_final: 0.5062 (p) REVERT: A 891 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.5581 (m-10) REVERT: B 188 GLN cc_start: 0.7003 (tp40) cc_final: 0.6698 (tp-100) REVERT: B 435 HIS cc_start: 0.7088 (OUTLIER) cc_final: 0.6152 (m-70) REVERT: B 891 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.5274 (m-10) outliers start: 31 outliers final: 17 residues processed: 146 average time/residue: 0.0986 time to fit residues: 23.4954 Evaluate side-chains 146 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 883 ILE Chi-restraints excluded: chain B residue 891 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 146 optimal weight: 0.4980 chunk 164 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** 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 = 0.4640 r_free = 0.4640 target = 0.185810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.163129 restraints weight = 26523.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.163428 restraints weight = 27345.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.164695 restraints weight = 22588.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.164424 restraints weight = 16856.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.164617 restraints weight = 14401.783| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 14370 Z= 0.102 Angle : 0.514 13.266 19420 Z= 0.251 Chirality : 0.037 0.153 2158 Planarity : 0.003 0.040 2476 Dihedral : 3.785 15.425 1898 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.99 % Allowed : 18.08 % Favored : 79.93 % 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: 0.59 (0.21), residues: 1706 helix: 0.93 (0.16), residues: 1144 sheet: None (None), residues: 0 loop : -0.60 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 255 TYR 0.012 0.001 TYR B 811 PHE 0.021 0.001 PHE A 232 TRP 0.008 0.001 TRP A 64 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00228 (14370) covalent geometry : angle 0.51410 (19420) hydrogen bonds : bond 0.03374 ( 758) hydrogen bonds : angle 3.57459 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.16 seconds wall clock time: 33 minutes 56.85 seconds (2036.85 seconds total)