Starting phenix.real_space_refine on Thu Jun 12 15:12:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qd8_13910/06_2025/7qd8_13910.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qd8_13910/06_2025/7qd8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qd8_13910/06_2025/7qd8_13910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qd8_13910/06_2025/7qd8_13910.map" model { file = "/net/cci-nas-00/data/ceres_data/7qd8_13910/06_2025/7qd8_13910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qd8_13910/06_2025/7qd8_13910.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 7.62, per 1000 atoms: 0.54 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: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.46 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: 4.04 Time building geometry restraints manager: 3.44 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: 0.06 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: 0.590 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.110 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- 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 : 5.28 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP B 102 HIS 0.007 0.001 HIS A 43 PHE 0.040 0.002 PHE B 891 TYR 0.027 0.002 TYR A 811 ARG 0.004 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.15568 ( 758) hydrogen bonds : angle 5.84669 ( 2235) covalent geometry : bond 0.00393 (14370) covalent geometry : angle 0.74485 (19420) *********************** 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 : 1.694 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: 0.2176 time to fit residues: 53.4786 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 : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 134 optimal weight: 0.0370 chunk 52 optimal weight: 0.0870 chunk 81 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 217 GLN B 43 HIS B 83 GLN B 116 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.188285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.166322 restraints weight = 26760.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.166427 restraints weight = 32238.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.167893 restraints weight = 24380.137| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14370 Z= 0.102 Angle : 0.478 7.347 19420 Z= 0.252 Chirality : 0.037 0.159 2158 Planarity : 0.004 0.054 2476 Dihedral : 4.109 15.710 1898 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.53 % Allowed : 7.28 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 1706 helix: -0.06 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.87 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 923 HIS 0.009 0.001 HIS A 38 PHE 0.020 0.001 PHE A 329 TYR 0.014 0.001 TYR B 387 ARG 0.002 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 758) hydrogen bonds : angle 3.97503 ( 2235) covalent geometry : bond 0.00212 (14370) covalent geometry : angle 0.47845 (19420) *********************** 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 149 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: A 295 ILE cc_start: 0.7767 (mm) cc_final: 0.7480 (mm) REVERT: A 456 TYR cc_start: 0.5243 (m-10) cc_final: 0.4527 (t80) outliers start: 8 outliers final: 1 residues processed: 146 average time/residue: 0.2017 time to fit residues: 48.0170 Evaluate side-chains 120 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 41 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** 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 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.179195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.155372 restraints weight = 26809.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.154688 restraints weight = 33178.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.156142 restraints weight = 26975.565| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14370 Z= 0.256 Angle : 0.677 8.014 19420 Z= 0.356 Chirality : 0.044 0.172 2158 Planarity : 0.005 0.052 2476 Dihedral : 4.862 17.515 1898 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.46 % Allowed : 12.38 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1706 helix: -0.24 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.97 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 528 HIS 0.010 0.001 HIS A 38 PHE 0.029 0.003 PHE B 891 TYR 0.023 0.002 TYR A 646 ARG 0.006 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.05200 ( 758) hydrogen bonds : angle 4.35768 ( 2235) covalent geometry : bond 0.00601 (14370) covalent geometry : angle 0.67679 (19420) *********************** 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 156 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 TYR cc_start: 0.5780 (m-10) cc_final: 0.4546 (t80) REVERT: A 891 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.6023 (m-80) REVERT: B 891 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6244 (m-10) outliers start: 22 outliers final: 12 residues processed: 146 average time/residue: 0.1994 time to fit residues: 47.9033 Evaluate side-chains 133 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 646 TYR 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 20 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 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 83 GLN A 116 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN 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 296 HIS ** 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 = 0.4625 r_free = 0.4625 target = 0.184420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.160774 restraints weight = 26616.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.160220 restraints weight = 32075.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.161838 restraints weight = 25999.148| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14370 Z= 0.117 Angle : 0.516 12.158 19420 Z= 0.263 Chirality : 0.038 0.151 2158 Planarity : 0.003 0.046 2476 Dihedral : 4.231 15.906 1898 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.92 % Allowed : 14.04 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1706 helix: 0.24 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -0.77 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 102 HIS 0.007 0.001 HIS A 38 PHE 0.016 0.002 PHE B 891 TYR 0.025 0.001 TYR A 819 ARG 0.002 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 758) hydrogen bonds : angle 3.83940 ( 2235) covalent geometry : bond 0.00263 (14370) covalent geometry : angle 0.51617 (19420) *********************** 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 157 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.596 Fit side-chains revert: symmetry clash REVERT: A 456 TYR cc_start: 0.5798 (m-10) cc_final: 0.4519 (t80) REVERT: A 891 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.5649 (m-10) REVERT: B 295 ILE cc_start: 0.7518 (mm) cc_final: 0.7310 (mm) REVERT: B 832 MET cc_start: 0.7222 (mmm) cc_final: 0.7000 (mmm) REVERT: B 891 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.5336 (m-10) outliers start: 29 outliers final: 16 residues processed: 149 average time/residue: 0.2454 time to fit residues: 58.4622 Evaluate side-chains 137 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 721 VAL 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 58 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 285 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 8 optimal weight: 0.1980 chunk 163 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.184001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.160715 restraints weight = 26634.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.160607 restraints weight = 31056.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.161576 restraints weight = 25771.478| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.2022 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= 0.124 Angle : 0.522 11.122 19420 Z= 0.265 Chirality : 0.038 0.153 2158 Planarity : 0.003 0.032 2476 Dihedral : 4.121 16.054 1898 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.32 % Allowed : 15.17 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1706 helix: 0.43 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -0.75 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 923 HIS 0.010 0.001 HIS B 38 PHE 0.017 0.002 PHE B 436 TYR 0.025 0.001 TYR B 819 ARG 0.002 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 758) hydrogen bonds : angle 3.74781 ( 2235) covalent geometry : bond 0.00282 (14370) covalent geometry : angle 0.52230 (19420) *********************** 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 165 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 435 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6757 (m-70) REVERT: A 456 TYR cc_start: 0.5695 (m-10) cc_final: 0.4530 (t80) REVERT: A 891 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.5629 (m-10) REVERT: B 295 ILE cc_start: 0.7346 (mm) cc_final: 0.7138 (mm) REVERT: B 891 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.5417 (m-10) outliers start: 35 outliers final: 23 residues processed: 157 average time/residue: 0.2145 time to fit residues: 53.8607 Evaluate side-chains 152 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 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 501 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 721 VAL 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 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 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 140 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 193 GLN ** 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 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.183786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.160014 restraints weight = 26878.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.159398 restraints weight = 31397.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.160787 restraints weight = 25774.518| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.2178 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= 0.129 Angle : 0.534 11.938 19420 Z= 0.269 Chirality : 0.038 0.158 2158 Planarity : 0.003 0.029 2476 Dihedral : 4.093 16.397 1898 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.05 % Allowed : 16.75 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1706 helix: 0.51 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -0.71 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 923 HIS 0.009 0.001 HIS B 38 PHE 0.017 0.002 PHE B 891 TYR 0.021 0.001 TYR B 819 ARG 0.002 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 758) hydrogen bonds : angle 3.72501 ( 2235) covalent geometry : bond 0.00296 (14370) covalent geometry : angle 0.53428 (19420) *********************** 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 157 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 435 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.6660 (m-70) REVERT: A 456 TYR cc_start: 0.5240 (m-10) cc_final: 0.4012 (t80) REVERT: A 891 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.5568 (m-10) REVERT: B 295 ILE cc_start: 0.7373 (mm) cc_final: 0.7161 (mm) REVERT: B 891 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.5401 (m-10) outliers start: 31 outliers final: 23 residues processed: 148 average time/residue: 0.2158 time to fit residues: 52.3200 Evaluate side-chains 147 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 576 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 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 469 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 576 THR 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 1 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 0.0000 chunk 153 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 170 optimal weight: 6.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.184594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.162375 restraints weight = 26530.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.162240 restraints weight = 32500.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.163271 restraints weight = 24499.371| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.2275 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= 0.116 Angle : 0.518 11.943 19420 Z= 0.260 Chirality : 0.038 0.155 2158 Planarity : 0.003 0.034 2476 Dihedral : 3.999 16.144 1898 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.32 % Allowed : 17.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1706 helix: 0.62 (0.16), residues: 1144 sheet: None (None), residues: 0 loop : -0.64 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 923 HIS 0.009 0.001 HIS B 38 PHE 0.023 0.002 PHE A 232 TYR 0.021 0.001 TYR A 811 ARG 0.003 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 758) hydrogen bonds : angle 3.65598 ( 2235) covalent geometry : bond 0.00263 (14370) covalent geometry : angle 0.51845 (19420) *********************** 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 163 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.620 Fit side-chains revert: symmetry clash REVERT: A 435 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6515 (m-70) REVERT: A 456 TYR cc_start: 0.5241 (m-10) cc_final: 0.4023 (t80) REVERT: A 891 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.5459 (m-10) REVERT: B 891 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.5279 (m-10) REVERT: B 941 PHE cc_start: 0.6143 (t80) cc_final: 0.5819 (t80) outliers start: 35 outliers final: 27 residues processed: 153 average time/residue: 0.2045 time to fit residues: 51.1185 Evaluate side-chains 153 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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 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 576 THR Chi-restraints excluded: chain A residue 629 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 811 TYR 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 285 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 576 THR 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 811 TYR 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 44 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** A 958 ASN ** 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** B 958 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.181351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.157213 restraints weight = 26577.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.156908 restraints weight = 31676.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.158319 restraints weight = 24617.101| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14370 Z= 0.169 Angle : 0.582 11.764 19420 Z= 0.295 Chirality : 0.040 0.164 2158 Planarity : 0.003 0.036 2476 Dihedral : 4.268 17.672 1898 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.45 % Allowed : 17.88 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1706 helix: 0.45 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -0.79 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 923 HIS 0.008 0.001 HIS B 38 PHE 0.023 0.002 PHE A 232 TYR 0.018 0.002 TYR A 811 ARG 0.003 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 758) hydrogen bonds : angle 3.87023 ( 2235) covalent geometry : bond 0.00396 (14370) covalent geometry : angle 0.58209 (19420) *********************** 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 166 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 ILE cc_start: 0.7383 (mm) cc_final: 0.7164 (mm) REVERT: A 435 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.6668 (m-70) REVERT: A 456 TYR cc_start: 0.5264 (m-10) cc_final: 0.4037 (t80) REVERT: A 597 THR cc_start: 0.5695 (OUTLIER) cc_final: 0.5171 (p) REVERT: A 891 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.5755 (m-10) REVERT: B 425 LYS cc_start: 0.5611 (mmtt) cc_final: 0.5092 (pttm) REVERT: B 435 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6050 (m-70) REVERT: B 597 THR cc_start: 0.5689 (OUTLIER) cc_final: 0.5164 (p) REVERT: B 891 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.5543 (m-10) REVERT: B 941 PHE cc_start: 0.5993 (t80) cc_final: 0.5676 (t80) outliers start: 37 outliers final: 26 residues processed: 155 average time/residue: 0.2244 time to fit residues: 55.8939 Evaluate side-chains 156 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE 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 359 MET 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 576 THR 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 29 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 501 ILE Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 597 THR 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 2 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN ** 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 958 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.184220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.160276 restraints weight = 26265.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.160040 restraints weight = 29209.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.161761 restraints weight = 24395.984| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14370 Z= 0.114 Angle : 0.535 12.612 19420 Z= 0.265 Chirality : 0.038 0.158 2158 Planarity : 0.003 0.039 2476 Dihedral : 4.005 15.943 1898 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.38 % Allowed : 18.28 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1706 helix: 0.66 (0.16), residues: 1142 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.009 0.001 HIS A 38 PHE 0.022 0.002 PHE A 232 TYR 0.014 0.001 TYR A 811 ARG 0.003 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 758) hydrogen bonds : angle 3.69551 ( 2235) covalent geometry : bond 0.00258 (14370) covalent geometry : angle 0.53539 (19420) *********************** 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 163 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6624 (m-70) REVERT: A 456 TYR cc_start: 0.5346 (m-10) cc_final: 0.4216 (t80) REVERT: A 597 THR cc_start: 0.5825 (OUTLIER) cc_final: 0.5201 (p) REVERT: A 891 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.5607 (m-10) REVERT: B 188 GLN cc_start: 0.6937 (tp40) cc_final: 0.6669 (tp-100) REVERT: B 435 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6053 (m-70) REVERT: B 597 THR cc_start: 0.5613 (OUTLIER) cc_final: 0.5163 (p) REVERT: B 891 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.5358 (m-10) REVERT: B 941 PHE cc_start: 0.5980 (t80) cc_final: 0.5694 (t80) outliers start: 36 outliers final: 24 residues processed: 153 average time/residue: 0.2111 time to fit residues: 52.9771 Evaluate side-chains 154 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 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 469 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 597 THR 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 29 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 501 ILE Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 597 THR 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 64 optimal weight: 0.0370 chunk 126 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 chunk 141 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 ** A 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.185863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.162270 restraints weight = 26610.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.161412 restraints weight = 30593.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.163853 restraints weight = 23592.193| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14370 Z= 0.102 Angle : 0.535 12.932 19420 Z= 0.261 Chirality : 0.037 0.154 2158 Planarity : 0.003 0.041 2476 Dihedral : 3.823 15.159 1898 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.92 % Allowed : 18.68 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1706 helix: 0.85 (0.16), residues: 1144 sheet: None (None), residues: 0 loop : -0.61 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.006 0.001 HIS B 38 PHE 0.021 0.001 PHE A 232 TYR 0.016 0.001 TYR B 811 ARG 0.003 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 758) hydrogen bonds : angle 3.58748 ( 2235) covalent geometry : bond 0.00229 (14370) covalent geometry : angle 0.53509 (19420) ********************** 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 156 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 TYR cc_start: 0.5178 (m-10) cc_final: 0.4187 (t80) REVERT: A 597 THR cc_start: 0.5799 (OUTLIER) cc_final: 0.5171 (p) REVERT: A 891 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.5670 (m-10) REVERT: B 188 GLN cc_start: 0.7428 (tp40) cc_final: 0.7062 (tp-100) REVERT: B 597 THR cc_start: 0.5745 (OUTLIER) cc_final: 0.5270 (p) REVERT: B 891 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.5231 (m-10) outliers start: 29 outliers final: 18 residues processed: 147 average time/residue: 0.2430 time to fit residues: 57.9042 Evaluate side-chains 143 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 501 ILE Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 620 ILE 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 53 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 142 optimal weight: 0.0010 chunk 72 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 246 ASN A 323 ASN ** A 924 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** ** 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 = 0.4633 r_free = 0.4633 target = 0.185288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.161680 restraints weight = 26785.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.161500 restraints weight = 29280.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.162583 restraints weight = 26552.194| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14370 Z= 0.108 Angle : 0.525 12.980 19420 Z= 0.256 Chirality : 0.037 0.152 2158 Planarity : 0.003 0.040 2476 Dihedral : 3.802 15.423 1898 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.72 % Allowed : 19.27 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1706 helix: 0.92 (0.16), residues: 1144 sheet: None (None), residues: 0 loop : -0.58 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 923 HIS 0.006 0.001 HIS A 38 PHE 0.021 0.001 PHE A 232 TYR 0.013 0.001 TYR B 811 ARG 0.003 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 758) hydrogen bonds : angle 3.58039 ( 2235) covalent geometry : bond 0.00246 (14370) covalent geometry : angle 0.52474 (19420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4118.94 seconds wall clock time: 74 minutes 41.99 seconds (4481.99 seconds total)