Starting phenix.real_space_refine on Wed Apr 8 04:55:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7b_31765/04_2026/7v7b_31765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7b_31765/04_2026/7v7b_31765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7b_31765/04_2026/7v7b_31765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7b_31765/04_2026/7v7b_31765.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7b_31765/04_2026/7v7b_31765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7b_31765/04_2026/7v7b_31765.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 222 5.16 5 C 22424 2.51 5 N 6022 2.21 5 O 6698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35366 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8809 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 47, 'TRANS': 1062} Chain breaks: 4 Chain: "B" Number of atoms: 8874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8874 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 41, 'TRANS': 1091} Chain breaks: 2 Restraints were copied for chains: C, D Time building chain proxies: 19.58, per 1000 atoms: 0.55 Number of scatterers: 35366 At special positions: 0 Unit cell: (217.109, 186.561, 154.922, 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 222 16.00 O 6698 8.00 N 6022 7.00 C 22424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1019 " - pdb=" SG CYS A1037 " distance=2.01 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 313 " distance=2.03 Simple disulfide: pdb=" SG CYS C1019 " - pdb=" SG CYS C1037 " distance=2.01 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 313 " distance=2.03 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: 3.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8436 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 64 sheets defined 25.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.657A pdb=" N SER A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A 42 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.762A pdb=" N GLY A 52 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A 53 " --> pdb=" O ARG A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 69 through 76 removed outlier: 4.030A pdb=" N HIS A 73 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 74 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.907A pdb=" N GLU A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.677A pdb=" N TYR A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 removed outlier: 3.757A pdb=" N LEU A 150 " --> pdb=" O SER A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 150' Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.554A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 166 through 191 removed outlier: 3.507A pdb=" N GLN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.938A pdb=" N LEU A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 350 Processing helix chain 'A' and resid 351 through 359 removed outlier: 3.583A pdb=" N MET A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.551A pdb=" N LYS A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.945A pdb=" N GLU A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 Processing helix chain 'A' and resid 409 through 419 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 435 through 452 removed outlier: 4.324A pdb=" N SER A 439 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'A' and resid 461 through 469 removed outlier: 4.027A pdb=" N ILE A 466 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYS A 467 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE A 468 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 removed outlier: 3.696A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.726A pdb=" N ASN A 488 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.701A pdb=" N GLN A 501 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.579A pdb=" N PHE A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 507 through 512' Processing helix chain 'A' and resid 515 through 541 removed outlier: 3.520A pdb=" N ALA A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 574 through 579 removed outlier: 3.614A pdb=" N TYR A 578 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.761A pdb=" N VAL A 590 " --> pdb=" O GLU A 586 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 591 " --> pdb=" O PRO A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 615 through 631 removed outlier: 3.728A pdb=" N THR A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 621 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.794A pdb=" N ILE A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 662 " --> pdb=" O GLY A 658 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 668 " --> pdb=" O GLY A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 690 removed outlier: 3.603A pdb=" N LYS A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS A 688 " --> pdb=" O ILE A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 removed outlier: 3.854A pdb=" N LEU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.917A pdb=" N VAL A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 738 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 766 removed outlier: 3.511A pdb=" N ILE A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA A 761 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 762 " --> pdb=" O ALA A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 removed outlier: 4.449A pdb=" N GLN A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 774 " --> pdb=" O THR A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 789 Processing helix chain 'A' and resid 801 through 816 removed outlier: 3.716A pdb=" N LYS A 807 " --> pdb=" O VAL A 803 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 811 " --> pdb=" O LYS A 807 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 840 removed outlier: 3.597A pdb=" N LYS A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 835 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 861 removed outlier: 3.534A pdb=" N LEU A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 860 " --> pdb=" O ASN A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 1003 through 1017 removed outlier: 4.466A pdb=" N THR A1009 " --> pdb=" O ASP A1005 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A1015 " --> pdb=" O TYR A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1057 removed outlier: 3.566A pdb=" N ARG A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1077 removed outlier: 3.744A pdb=" N ARG A1073 " --> pdb=" O GLY A1069 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A1075 " --> pdb=" O PHE A1071 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A1077 " --> pdb=" O ARG A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1220 removed outlier: 3.868A pdb=" N ALA A1220 " --> pdb=" O PRO A1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1059 removed outlier: 3.898A pdb=" N ASP B1053 " --> pdb=" O ASN B1049 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET B1054 " --> pdb=" O LEU B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1074 Processing helix chain 'B' and resid 1091 through 1095 Processing helix chain 'B' and resid 1096 through 1098 No H-bonds generated for 'chain 'B' and resid 1096 through 1098' Processing helix chain 'B' and resid 1101 through 1109 removed outlier: 4.561A pdb=" N GLU B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B1108 " --> pdb=" O LYS B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1138 removed outlier: 4.169A pdb=" N LYS B1131 " --> pdb=" O ASP B1127 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1133 " --> pdb=" O LEU B1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 35 through 48 removed outlier: 3.656A pdb=" N SER C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 removed outlier: 3.762A pdb=" N GLY C 52 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP C 53 " --> pdb=" O ARG C 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 49 through 53' Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 69 through 76 removed outlier: 4.031A pdb=" N HIS C 73 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 74 " --> pdb=" O MET C 70 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.907A pdb=" N GLU C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 137 " --> pdb=" O PHE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 146 removed outlier: 3.677A pdb=" N TYR C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 150 removed outlier: 3.758A pdb=" N LEU C 150 " --> pdb=" O SER C 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 150' Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.555A pdb=" N ASN C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 166 through 191 removed outlier: 3.508A pdb=" N GLN C 170 " --> pdb=" O ASP C 166 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 173 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE C 174 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 187 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.938A pdb=" N LEU C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 350 Processing helix chain 'C' and resid 351 through 359 removed outlier: 3.584A pdb=" N MET C 356 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.552A pdb=" N LYS C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 removed outlier: 3.944A pdb=" N GLU C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 401 Processing helix chain 'C' and resid 409 through 419 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 435 through 452 removed outlier: 4.324A pdb=" N SER C 439 " --> pdb=" O HIS C 435 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP C 447 " --> pdb=" O ASN C 443 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 452 " --> pdb=" O LEU C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 Processing helix chain 'C' and resid 461 through 469 removed outlier: 4.027A pdb=" N ILE C 466 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS C 467 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE C 468 " --> pdb=" O SER C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 removed outlier: 3.697A pdb=" N LEU C 474 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 491 removed outlier: 3.726A pdb=" N ASN C 488 " --> pdb=" O ARG C 484 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU C 489 " --> pdb=" O ARG C 485 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 501 removed outlier: 3.700A pdb=" N GLN C 501 " --> pdb=" O LEU C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 512 removed outlier: 3.579A pdb=" N PHE C 511 " --> pdb=" O ASP C 507 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 512 " --> pdb=" O ASP C 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 507 through 512' Processing helix chain 'C' and resid 515 through 541 removed outlier: 3.520A pdb=" N ALA C 533 " --> pdb=" O GLU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 574 through 579 removed outlier: 3.614A pdb=" N TYR C 578 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 595 removed outlier: 3.761A pdb=" N VAL C 590 " --> pdb=" O GLU C 586 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C 591 " --> pdb=" O PRO C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 607 Processing helix chain 'C' and resid 615 through 631 removed outlier: 3.727A pdb=" N THR C 619 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 620 " --> pdb=" O ARG C 616 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG C 621 " --> pdb=" O ASN C 617 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 626 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 627 " --> pdb=" O ALA C 623 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE C 629 " --> pdb=" O ASP C 625 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 630 " --> pdb=" O VAL C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 639 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.794A pdb=" N ILE C 661 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 662 " --> pdb=" O GLY C 658 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 690 removed outlier: 3.602A pdb=" N LYS C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C 683 " --> pdb=" O LYS C 679 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE C 684 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 685 " --> pdb=" O ALA C 681 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS C 688 " --> pdb=" O ILE C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 732 removed outlier: 3.854A pdb=" N LEU C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.917A pdb=" N VAL C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 738 " --> pdb=" O GLY C 734 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C 739 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER C 740 " --> pdb=" O LYS C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 766 removed outlier: 3.511A pdb=" N ILE C 754 " --> pdb=" O ASP C 750 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C 755 " --> pdb=" O ALA C 751 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 756 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 757 " --> pdb=" O GLN C 753 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 760 " --> pdb=" O ALA C 756 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA C 761 " --> pdb=" O LEU C 757 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 762 " --> pdb=" O ALA C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 776 removed outlier: 4.449A pdb=" N GLN C 773 " --> pdb=" O SER C 769 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 774 " --> pdb=" O THR C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 789 Processing helix chain 'C' and resid 801 through 816 removed outlier: 3.716A pdb=" N LYS C 807 " --> pdb=" O VAL C 803 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU C 811 " --> pdb=" O LYS C 807 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 816 " --> pdb=" O LEU C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 840 removed outlier: 3.597A pdb=" N LYS C 834 " --> pdb=" O ALA C 830 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA C 835 " --> pdb=" O ARG C 831 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 839 " --> pdb=" O ALA C 835 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 861 removed outlier: 3.534A pdb=" N LEU C 852 " --> pdb=" O LYS C 848 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 853 " --> pdb=" O GLU C 849 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 860 " --> pdb=" O ASN C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 872 Processing helix chain 'C' and resid 1003 through 1017 removed outlier: 4.465A pdb=" N THR C1009 " --> pdb=" O ASP C1005 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C1012 " --> pdb=" O ILE C1008 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C1014 " --> pdb=" O GLU C1010 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C1015 " --> pdb=" O TYR C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1057 removed outlier: 3.565A pdb=" N ARG C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1077 removed outlier: 3.744A pdb=" N ARG C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C1075 " --> pdb=" O PHE C1071 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C1077 " --> pdb=" O ARG C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1220 removed outlier: 3.869A pdb=" N ALA C1220 " --> pdb=" O PRO C1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1059 removed outlier: 3.898A pdb=" N ASP D1053 " --> pdb=" O ASN D1049 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D1054 " --> pdb=" O LEU D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1069 through 1074 Processing helix chain 'D' and resid 1091 through 1095 Processing helix chain 'D' and resid 1096 through 1098 No H-bonds generated for 'chain 'D' and resid 1096 through 1098' Processing helix chain 'D' and resid 1101 through 1109 removed outlier: 4.561A pdb=" N GLU D1107 " --> pdb=" O PRO D1103 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D1108 " --> pdb=" O LYS D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1125 through 1138 removed outlier: 4.168A pdb=" N LYS D1131 " --> pdb=" O ASP D1127 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D1133 " --> pdb=" O LEU D1129 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 645 through 647 removed outlier: 3.955A pdb=" N VAL A 646 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 654 " --> pdb=" O VAL A 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1085 through 1086 removed outlier: 6.229A pdb=" N ASN A1371 " --> pdb=" O ILE A1354 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE A1354 " --> pdb=" O ASN A1371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1096 through 1098 removed outlier: 6.334A pdb=" N GLY A1111 " --> pdb=" O THR A1097 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1116 through 1120 removed outlier: 3.634A pdb=" N LEU A1119 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA A1129 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1141 through 1143 removed outlier: 3.584A pdb=" N THR A1152 " --> pdb=" O ALA A1162 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A1176 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A1163 " --> pdb=" O HIS A1174 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS A1174 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1181 through 1184 removed outlier: 3.630A pdb=" N VAL A1192 " --> pdb=" O TYR A1203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A1196 " --> pdb=" O ILE A1199 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA A1200 " --> pdb=" O THR A1213 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR A1213 " --> pdb=" O ALA A1200 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A1202 " --> pdb=" O LEU A1211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1242 through 1245 removed outlier: 4.049A pdb=" N HIS A1253 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP A1245 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA A1251 " --> pdb=" O ASP A1245 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1265 through 1266 removed outlier: 3.548A pdb=" N ILE A1279 " --> pdb=" O HIS A1289 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS A1289 " --> pdb=" O ILE A1279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1297 through 1301 Processing sheet with id=AB1, first strand: chain 'B' and resid 1004 through 1008 removed outlier: 6.003A pdb=" N GLY B1031 " --> pdb=" O ASN B1005 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE B1007 " --> pdb=" O LEU B1029 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B1029 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLY B1026 " --> pdb=" O SER B1042 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER B1042 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B1030 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B1038 " --> pdb=" O PHE B1030 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 18 through 25 removed outlier: 3.508A pdb=" N VAL B 19 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 21 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE B 23 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N ASP B 28 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU B 29 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 31 " --> pdb=" O TYR B 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 41 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 53 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL B 43 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 63 through 67 removed outlier: 4.100A pdb=" N VAL B 63 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 65 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 78 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 86 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N HIS B 105 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 132 through 134 removed outlier: 3.907A pdb=" N ILE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.443A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 178 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 193 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 218 through 222 removed outlier: 3.764A pdb=" N MET B 218 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 222 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY B 228 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 237 through 240 removed outlier: 3.723A pdb=" N ILE B 237 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 261 through 263 removed outlier: 3.771A pdb=" N ASN B 262 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 272 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU B 280 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU B 304 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N MET B 282 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B 302 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 284 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 300 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU B 286 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 313 through 318 removed outlier: 3.559A pdb=" N GLY B 325 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 315 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 362 through 365 Processing sheet with id=AC2, first strand: chain 'B' and resid 409 through 410 removed outlier: 3.756A pdb=" N GLY B 409 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 442 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 469 through 471 Processing sheet with id=AC4, first strand: chain 'B' and resid 507 through 508 removed outlier: 3.705A pdb=" N GLU B 525 " --> pdb=" O HIS B 522 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AC6, first strand: chain 'B' and resid 568 through 569 removed outlier: 3.520A pdb=" N HIS B 578 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 589 through 595 removed outlier: 4.224A pdb=" N ILE B 591 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B 603 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N MET B 593 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR B 601 " --> pdb=" O MET B 593 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS B 604 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 612 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 637 through 640 removed outlier: 3.500A pdb=" N THR B 657 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 735 through 736 removed outlier: 6.368A pdb=" N LEU B 791 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA B 804 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE B 793 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER B 764 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 739 through 741 Processing sheet with id=AD2, first strand: chain 'B' and resid 811 through 817 removed outlier: 5.714A pdb=" N ALA B 813 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA B 834 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 815 " --> pdb=" O GLY B 832 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 847 " --> pdb=" O THR B 833 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE B 848 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU B 863 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 850 " --> pdb=" O VAL B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 870 through 876 removed outlier: 4.253A pdb=" N SER B 872 " --> pdb=" O SER B 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 913 through 917 removed outlier: 3.625A pdb=" N LYS B 917 " --> pdb=" O PHE B 920 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 920 " --> pdb=" O LYS B 917 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 957 through 959 removed outlier: 4.346A pdb=" N GLY B 996 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 645 through 647 removed outlier: 3.956A pdb=" N VAL C 646 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 654 " --> pdb=" O VAL C 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 1085 through 1086 removed outlier: 6.229A pdb=" N ASN C1371 " --> pdb=" O ILE C1354 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C1354 " --> pdb=" O ASN C1371 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1096 through 1098 removed outlier: 6.334A pdb=" N GLY C1111 " --> pdb=" O THR C1097 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1116 through 1120 removed outlier: 3.633A pdb=" N LEU C1119 " --> pdb=" O ALA C1129 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA C1129 " --> pdb=" O LEU C1119 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1141 through 1143 removed outlier: 3.583A pdb=" N THR C1152 " --> pdb=" O ALA C1162 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE C1176 " --> pdb=" O SER C1161 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C1163 " --> pdb=" O HIS C1174 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS C1174 " --> pdb=" O LEU C1163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1181 through 1184 removed outlier: 3.631A pdb=" N VAL C1192 " --> pdb=" O TYR C1203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS C1196 " --> pdb=" O ILE C1199 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA C1200 " --> pdb=" O THR C1213 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR C1213 " --> pdb=" O ALA C1200 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C1202 " --> pdb=" O LEU C1211 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1242 through 1245 removed outlier: 4.049A pdb=" N HIS C1253 " --> pdb=" O LEU C1243 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP C1245 " --> pdb=" O ALA C1251 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA C1251 " --> pdb=" O ASP C1245 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1265 through 1266 removed outlier: 3.548A pdb=" N ILE C1279 " --> pdb=" O HIS C1289 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS C1289 " --> pdb=" O ILE C1279 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1297 through 1301 Processing sheet with id=AE6, first strand: chain 'D' and resid 1004 through 1008 removed outlier: 6.002A pdb=" N GLY D1031 " --> pdb=" O ASN D1005 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE D1007 " --> pdb=" O LEU D1029 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU D1029 " --> pdb=" O PHE D1007 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLY D1026 " --> pdb=" O SER D1042 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER D1042 " --> pdb=" O GLY D1026 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D1030 " --> pdb=" O GLY D1038 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY D1038 " --> pdb=" O PHE D1030 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 18 through 25 removed outlier: 3.508A pdb=" N VAL D 19 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 21 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE D 23 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N ASP D 28 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU D 29 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 31 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 41 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS D 53 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL D 43 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 63 through 67 removed outlier: 4.099A pdb=" N VAL D 63 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 65 " --> pdb=" O PHE D 78 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 78 " --> pdb=" O GLU D 65 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA D 86 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N HIS D 105 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE D 88 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 132 through 134 removed outlier: 3.906A pdb=" N ILE D 157 " --> pdb=" O PHE D 140 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 164 through 169 removed outlier: 6.443A pdb=" N VAL D 181 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 167 " --> pdb=" O CYS D 179 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS D 179 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE D 169 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR D 177 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 178 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR D 193 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 218 through 222 removed outlier: 3.765A pdb=" N MET D 218 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 222 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY D 228 " --> pdb=" O VAL D 222 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 237 through 240 removed outlier: 3.723A pdb=" N ILE D 237 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 261 through 263 removed outlier: 3.770A pdb=" N ASN D 262 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 272 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU D 280 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU D 304 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N MET D 282 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL D 302 " --> pdb=" O MET D 282 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU D 284 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU D 300 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU D 286 " --> pdb=" O LYS D 298 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 313 through 318 removed outlier: 3.560A pdb=" N GLY D 325 " --> pdb=" O CYS D 313 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR D 315 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 362 through 365 Processing sheet with id=AF7, first strand: chain 'D' and resid 409 through 410 removed outlier: 3.757A pdb=" N GLY D 409 " --> pdb=" O SER D 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU D 442 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 469 through 471 Processing sheet with id=AF9, first strand: chain 'D' and resid 507 through 508 removed outlier: 3.705A pdb=" N GLU D 525 " --> pdb=" O HIS D 522 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 511 through 512 Processing sheet with id=AG2, first strand: chain 'D' and resid 568 through 569 removed outlier: 3.520A pdb=" N HIS D 578 " --> pdb=" O ILE D 568 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 589 through 595 removed outlier: 4.224A pdb=" N ILE D 591 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU D 603 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N MET D 593 " --> pdb=" O TYR D 601 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR D 601 " --> pdb=" O MET D 593 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N CYS D 604 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 612 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 637 through 640 Processing sheet with id=AG5, first strand: chain 'D' and resid 735 through 736 removed outlier: 6.368A pdb=" N LEU D 791 " --> pdb=" O ALA D 804 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA D 804 " --> pdb=" O LEU D 791 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 793 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER D 764 " --> pdb=" O GLN D 806 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 739 through 741 Processing sheet with id=AG7, first strand: chain 'D' and resid 811 through 817 removed outlier: 5.715A pdb=" N ALA D 813 " --> pdb=" O ALA D 834 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA D 834 " --> pdb=" O ALA D 813 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 815 " --> pdb=" O GLY D 832 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG D 847 " --> pdb=" O THR D 833 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE D 848 " --> pdb=" O GLU D 863 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D 863 " --> pdb=" O ILE D 848 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL D 850 " --> pdb=" O VAL D 861 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 870 through 876 removed outlier: 4.253A pdb=" N SER D 872 " --> pdb=" O SER D 883 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 913 through 917 removed outlier: 3.624A pdb=" N LYS D 917 " --> pdb=" O PHE D 920 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 920 " --> pdb=" O LYS D 917 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 957 through 959 removed outlier: 4.347A pdb=" N GLY D 996 " --> pdb=" O VAL D 976 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN D 978 " --> pdb=" O GLU D 994 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLU D 994 " --> pdb=" O GLN D 978 " (cutoff:3.500A) 883 hydrogen bonds defined for protein. 2352 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: 10.32 Time building geometry restraints manager: 4.28 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: 11560 1.34 - 1.46: 6649 1.46 - 1.58: 17497 1.58 - 1.70: 0 1.70 - 1.82: 340 Bond restraints: 36046 Sorted by residual: bond pdb=" C LEU D 571 " pdb=" N PRO D 572 " ideal model delta sigma weight residual 1.336 1.373 -0.038 1.23e-02 6.61e+03 9.47e+00 bond pdb=" C LEU B 571 " pdb=" N PRO B 572 " ideal model delta sigma weight residual 1.336 1.373 -0.038 1.23e-02 6.61e+03 9.34e+00 bond pdb=" C HIS A 433 " pdb=" N PRO A 434 " ideal model delta sigma weight residual 1.332 1.368 -0.037 1.33e-02 5.65e+03 7.63e+00 bond pdb=" C HIS C 433 " pdb=" N PRO C 434 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.33e-02 5.65e+03 7.34e+00 bond pdb=" C GLU B 224 " pdb=" N PRO B 225 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.16e+00 ... (remaining 36041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 47260 2.22 - 4.44: 1334 4.44 - 6.66: 160 6.66 - 8.88: 58 8.88 - 11.11: 8 Bond angle restraints: 48820 Sorted by residual: angle pdb=" C ARG A 545 " pdb=" N THR A 546 " pdb=" CA THR A 546 " ideal model delta sigma weight residual 121.54 131.56 -10.02 1.91e+00 2.74e-01 2.75e+01 angle pdb=" C ARG C 545 " pdb=" N THR C 546 " pdb=" CA THR C 546 " ideal model delta sigma weight residual 121.54 131.54 -10.00 1.91e+00 2.74e-01 2.74e+01 angle pdb=" N LEU C 343 " pdb=" CA LEU C 343 " pdb=" C LEU C 343 " ideal model delta sigma weight residual 114.56 108.14 6.42 1.27e+00 6.20e-01 2.55e+01 angle pdb=" N LEU A 343 " pdb=" CA LEU A 343 " pdb=" C LEU A 343 " ideal model delta sigma weight residual 114.56 108.18 6.38 1.27e+00 6.20e-01 2.52e+01 angle pdb=" N ILE A1205 " pdb=" CA ILE A1205 " pdb=" C ILE A1205 " ideal model delta sigma weight residual 113.42 107.55 5.87 1.17e+00 7.31e-01 2.52e+01 ... (remaining 48815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 20905 16.08 - 32.16: 745 32.16 - 48.23: 166 48.23 - 64.31: 2 64.31 - 80.39: 10 Dihedral angle restraints: 21828 sinusoidal: 8790 harmonic: 13038 Sorted by residual: dihedral pdb=" CA ARG D 589 " pdb=" C ARG D 589 " pdb=" N SER D 590 " pdb=" CA SER D 590 " ideal model delta harmonic sigma weight residual -180.00 -138.68 -41.32 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA ARG B 589 " pdb=" C ARG B 589 " pdb=" N SER B 590 " pdb=" CA SER B 590 " ideal model delta harmonic sigma weight residual -180.00 -138.72 -41.28 0 5.00e+00 4.00e-02 6.82e+01 dihedral pdb=" CA PHE B 180 " pdb=" C PHE B 180 " pdb=" N VAL B 181 " pdb=" CA VAL B 181 " ideal model delta harmonic sigma weight residual 180.00 148.82 31.18 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 21825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3799 0.048 - 0.097: 1330 0.097 - 0.145: 412 0.145 - 0.193: 49 0.193 - 0.242: 6 Chirality restraints: 5596 Sorted by residual: chirality pdb=" CB ILE A 568 " pdb=" CA ILE A 568 " pdb=" CG1 ILE A 568 " pdb=" CG2 ILE A 568 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE C 568 " pdb=" CA ILE C 568 " pdb=" CG1 ILE C 568 " pdb=" CG2 ILE C 568 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ASP A 826 " pdb=" N ASP A 826 " pdb=" C ASP A 826 " pdb=" CB ASP A 826 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 5593 not shown) Planarity restraints: 6294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 928 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C ARG B 928 " -0.049 2.00e-02 2.50e+03 pdb=" O ARG B 928 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B 929 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 928 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ARG D 928 " -0.048 2.00e-02 2.50e+03 pdb=" O ARG D 928 " 0.018 2.00e-02 2.50e+03 pdb=" N SER D 929 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 586 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO A 587 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " -0.035 5.00e-02 4.00e+02 ... (remaining 6291 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3903 2.75 - 3.29: 32053 3.29 - 3.83: 55521 3.83 - 4.36: 65308 4.36 - 4.90: 110579 Nonbonded interactions: 267364 Sorted by model distance: nonbonded pdb=" OG SER B 737 " pdb=" OD1 ASN B 790 " model vdw 2.216 3.040 nonbonded pdb=" OG SER D 737 " pdb=" OD1 ASN D 790 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLU A1272 " pdb=" OH TYR A1342 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU C1272 " pdb=" OH TYR C1342 " model vdw 2.269 3.040 nonbonded pdb=" O LEU C 592 " pdb=" OG SER C 595 " model vdw 2.275 3.040 ... (remaining 267359 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.890 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 47.660 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 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 0.062 36050 Z= 0.217 Angle : 0.916 11.106 48828 Z= 0.518 Chirality : 0.053 0.242 5596 Planarity : 0.007 0.064 6294 Dihedral : 9.450 80.389 13380 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.94 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.89 (0.10), residues: 4454 helix: -4.15 (0.08), residues: 970 sheet: -2.50 (0.15), residues: 1034 loop : -3.25 (0.10), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1087 TYR 0.018 0.002 TYR A 808 PHE 0.023 0.002 PHE D 226 TRP 0.028 0.003 TRP A 447 HIS 0.008 0.002 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00443 (36046) covalent geometry : angle 0.91598 (48820) SS BOND : bond 0.01494 ( 4) SS BOND : angle 1.93521 ( 8) hydrogen bonds : bond 0.30454 ( 883) hydrogen bonds : angle 10.94705 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1103 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.4683 (t0) cc_final: 0.4112 (m-30) REVERT: A 85 MET cc_start: 0.1328 (tpt) cc_final: -0.0113 (ttm) REVERT: A 179 LEU cc_start: 0.7697 (tp) cc_final: 0.7454 (tp) REVERT: A 753 GLN cc_start: 0.7730 (mt0) cc_final: 0.7453 (mt0) REVERT: A 773 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7140 (mm-40) REVERT: A 1166 MET cc_start: 0.1184 (mmm) cc_final: 0.0631 (ptm) REVERT: A 1288 LEU cc_start: 0.8270 (mp) cc_final: 0.8024 (tt) REVERT: A 1304 THR cc_start: 0.7587 (p) cc_final: 0.7182 (t) REVERT: B 166 ASP cc_start: 0.8585 (t0) cc_final: 0.8312 (t70) REVERT: B 182 TYR cc_start: 0.7132 (t80) cc_final: 0.6123 (t80) REVERT: B 246 LEU cc_start: 0.7909 (mp) cc_final: 0.7701 (mp) REVERT: B 284 LEU cc_start: 0.7072 (mp) cc_final: 0.6786 (mp) REVERT: B 355 ASN cc_start: 0.8508 (t0) cc_final: 0.8163 (t0) REVERT: B 693 LEU cc_start: 0.5534 (mp) cc_final: 0.4037 (mp) REVERT: B 723 LYS cc_start: 0.6938 (mttm) cc_final: 0.6297 (mmtp) REVERT: B 860 THR cc_start: 0.6317 (m) cc_final: 0.5832 (m) REVERT: B 973 ASN cc_start: 0.7783 (m-40) cc_final: 0.7539 (m-40) REVERT: B 1048 TYR cc_start: 0.7646 (t80) cc_final: 0.7422 (t80) REVERT: B 1114 TYR cc_start: 0.5545 (t80) cc_final: 0.5175 (t80) REVERT: C 9 ASP cc_start: 0.4792 (t0) cc_final: 0.4126 (m-30) REVERT: C 85 MET cc_start: 0.1262 (tpt) cc_final: -0.0165 (ttm) REVERT: C 179 LEU cc_start: 0.7748 (tp) cc_final: 0.7508 (tp) REVERT: C 753 GLN cc_start: 0.7735 (mt0) cc_final: 0.7404 (mt0) REVERT: C 773 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7034 (mm-40) REVERT: C 1084 SER cc_start: 0.7389 (p) cc_final: 0.7175 (p) REVERT: C 1166 MET cc_start: 0.1149 (mmm) cc_final: 0.0607 (ptm) REVERT: C 1288 LEU cc_start: 0.8270 (mp) cc_final: 0.8055 (tt) REVERT: C 1304 THR cc_start: 0.7520 (p) cc_final: 0.7130 (t) REVERT: D 182 TYR cc_start: 0.7090 (t80) cc_final: 0.5829 (t80) REVERT: D 213 GLU cc_start: 0.8463 (tt0) cc_final: 0.8192 (tp30) REVERT: D 355 ASN cc_start: 0.8491 (t0) cc_final: 0.8114 (t0) REVERT: D 606 LEU cc_start: 0.6545 (mm) cc_final: 0.6319 (mt) REVERT: D 722 ARG cc_start: 0.5019 (mmm160) cc_final: 0.4696 (mmm160) REVERT: D 860 THR cc_start: 0.6427 (m) cc_final: 0.6004 (m) REVERT: D 973 ASN cc_start: 0.7972 (m-40) cc_final: 0.7579 (m-40) REVERT: D 1097 PHE cc_start: 0.6553 (t80) cc_final: 0.6335 (t80) REVERT: D 1114 TYR cc_start: 0.5596 (t80) cc_final: 0.5285 (t80) outliers start: 0 outliers final: 0 residues processed: 1103 average time/residue: 0.2325 time to fit residues: 403.4578 Evaluate side-chains 618 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0060 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 433 HIS A 497 ASN A 553 HIS ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1174 HIS A1201 HIS A1222 ASN A1253 HIS A1261 ASN A1289 HIS ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 672 ASN B 677 ASN B 905 HIS B1055 GLN C 102 ASN C 433 HIS C 553 HIS ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1015 GLN C1201 HIS C1253 HIS C1261 ASN C1289 HIS ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 467 GLN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 672 ASN D 677 ASN D 803 HIS D 905 HIS D1055 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.189297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.162459 restraints weight = 70717.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.160882 restraints weight = 81028.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.163016 restraints weight = 68349.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.163599 restraints weight = 47418.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.163848 restraints weight = 40613.209| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36050 Z= 0.122 Angle : 0.650 9.562 48828 Z= 0.340 Chirality : 0.045 0.165 5596 Planarity : 0.005 0.052 6294 Dihedral : 5.894 32.911 4816 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.11), residues: 4454 helix: -2.83 (0.12), residues: 1026 sheet: -2.00 (0.16), residues: 1000 loop : -2.94 (0.11), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1102 TYR 0.025 0.001 TYR C1223 PHE 0.019 0.001 PHE A1301 TRP 0.022 0.002 TRP A 726 HIS 0.006 0.001 HIS A1134 Details of bonding type rmsd covalent geometry : bond 0.00259 (36046) covalent geometry : angle 0.64941 (48820) SS BOND : bond 0.00135 ( 4) SS BOND : angle 1.09057 ( 8) hydrogen bonds : bond 0.04605 ( 883) hydrogen bonds : angle 7.10181 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 791 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.4256 (t0) cc_final: 0.4024 (m-30) REVERT: A 85 MET cc_start: 0.0810 (tpt) cc_final: -0.0883 (ttm) REVERT: A 113 MET cc_start: 0.4401 (ptm) cc_final: 0.4015 (ppp) REVERT: A 773 GLN cc_start: 0.7438 (tm-30) cc_final: 0.7108 (mp10) REVERT: A 814 GLU cc_start: 0.8162 (tp30) cc_final: 0.7840 (tp30) REVERT: A 1109 MET cc_start: 0.6238 (ptp) cc_final: 0.5975 (ptp) REVERT: A 1166 MET cc_start: 0.0880 (mmm) cc_final: 0.0349 (ptm) REVERT: A 1186 LYS cc_start: 0.5314 (mmmt) cc_final: 0.4719 (mmmm) REVERT: A 1288 LEU cc_start: 0.8021 (mp) cc_final: 0.7639 (tt) REVERT: A 1304 THR cc_start: 0.7527 (p) cc_final: 0.7096 (t) REVERT: B 182 TYR cc_start: 0.6743 (t80) cc_final: 0.6029 (t80) REVERT: B 449 MET cc_start: 0.0488 (mmm) cc_final: 0.0140 (mmp) REVERT: B 679 MET cc_start: 0.5098 (mmm) cc_final: 0.4401 (tmm) REVERT: B 723 LYS cc_start: 0.6930 (mttm) cc_final: 0.6372 (mmtp) REVERT: B 894 THR cc_start: 0.5367 (t) cc_final: 0.4994 (p) REVERT: B 916 THR cc_start: 0.7581 (p) cc_final: 0.7355 (t) REVERT: B 929 SER cc_start: 0.8318 (m) cc_final: 0.8017 (t) REVERT: B 1092 ASP cc_start: 0.8537 (m-30) cc_final: 0.8123 (m-30) REVERT: B 1105 MET cc_start: 0.6019 (mtt) cc_final: 0.5633 (mtt) REVERT: B 1114 TYR cc_start: 0.5738 (t80) cc_final: 0.5262 (t80) REVERT: C 9 ASP cc_start: 0.4254 (t0) cc_final: 0.4010 (m-30) REVERT: C 85 MET cc_start: 0.0583 (tpt) cc_final: -0.1097 (ttm) REVERT: C 113 MET cc_start: 0.4367 (ptm) cc_final: 0.4009 (ppp) REVERT: C 616 ARG cc_start: 0.6463 (ptt-90) cc_final: 0.5419 (ptt90) REVERT: C 773 GLN cc_start: 0.7437 (tm-30) cc_final: 0.7033 (mp10) REVERT: C 814 GLU cc_start: 0.8063 (tp30) cc_final: 0.7833 (tp30) REVERT: C 1109 MET cc_start: 0.6329 (ptp) cc_final: 0.6083 (ptp) REVERT: C 1166 MET cc_start: 0.0889 (mmm) cc_final: 0.0335 (ptm) REVERT: C 1186 LYS cc_start: 0.5350 (mmmt) cc_final: 0.4741 (mmmm) REVERT: C 1285 PHE cc_start: 0.6654 (m-80) cc_final: 0.6441 (m-80) REVERT: C 1304 THR cc_start: 0.7429 (p) cc_final: 0.7044 (t) REVERT: D 141 LYS cc_start: 0.7454 (mttt) cc_final: 0.7163 (mttp) REVERT: D 182 TYR cc_start: 0.7010 (t80) cc_final: 0.5976 (t80) REVERT: D 213 GLU cc_start: 0.8418 (tt0) cc_final: 0.8185 (tp30) REVERT: D 606 LEU cc_start: 0.6328 (mm) cc_final: 0.6126 (mt) REVERT: D 679 MET cc_start: 0.5421 (mmm) cc_final: 0.4497 (tmm) REVERT: D 835 MET cc_start: 0.7812 (mmm) cc_final: 0.7382 (mmm) REVERT: D 916 THR cc_start: 0.7883 (p) cc_final: 0.7614 (t) REVERT: D 973 ASN cc_start: 0.7820 (m-40) cc_final: 0.7469 (m-40) REVERT: D 1092 ASP cc_start: 0.8641 (m-30) cc_final: 0.8307 (m-30) REVERT: D 1114 TYR cc_start: 0.5939 (t80) cc_final: 0.5645 (t80) outliers start: 3 outliers final: 2 residues processed: 794 average time/residue: 0.2277 time to fit residues: 289.7279 Evaluate side-chains 541 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 539 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 308 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 417 optimal weight: 6.9990 chunk 300 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 394 HIS A 687 ASN A 773 GLN A 788 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 HIS A1201 HIS A1221 ASN ** A1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 163 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B 759 GLN B 796 GLN B 803 HIS B 885 ASN B 993 GLN B1005 ASN C 183 GLN C 394 HIS C 497 ASN C 687 ASN C 773 GLN C 788 GLN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1174 HIS C1201 HIS ** C1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN D 163 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 GLN D 708 GLN D 759 GLN D 796 GLN D 885 ASN ** D 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN D1034 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.181838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.153929 restraints weight = 71259.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.152606 restraints weight = 86780.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.154802 restraints weight = 71507.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.154419 restraints weight = 49926.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.154835 restraints weight = 46711.594| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 36050 Z= 0.200 Angle : 0.711 10.405 48828 Z= 0.370 Chirality : 0.047 0.292 5596 Planarity : 0.005 0.070 6294 Dihedral : 6.019 30.839 4816 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.81 % Favored : 90.17 % Rotamer: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.11), residues: 4454 helix: -2.19 (0.14), residues: 1044 sheet: -1.89 (0.16), residues: 1002 loop : -2.96 (0.11), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 655 TYR 0.063 0.002 TYR C1223 PHE 0.027 0.002 PHE C1077 TRP 0.039 0.002 TRP C 135 HIS 0.009 0.002 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00456 (36046) covalent geometry : angle 0.71051 (48820) SS BOND : bond 0.00611 ( 4) SS BOND : angle 1.52162 ( 8) hydrogen bonds : bond 0.04268 ( 883) hydrogen bonds : angle 6.76827 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 669 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.1917 (tpt) cc_final: 0.0266 (ttm) REVERT: A 135 TRP cc_start: 0.7385 (m-10) cc_final: 0.7159 (m-90) REVERT: A 514 ARG cc_start: 0.6091 (mtt180) cc_final: 0.5602 (ttm-80) REVERT: A 602 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7507 (tp-100) REVERT: A 753 GLN cc_start: 0.7212 (mt0) cc_final: 0.6993 (mt0) REVERT: A 1166 MET cc_start: 0.0666 (mmm) cc_final: -0.0171 (ptm) REVERT: A 1288 LEU cc_start: 0.8310 (mp) cc_final: 0.8077 (tt) REVERT: A 1304 THR cc_start: 0.7488 (p) cc_final: 0.7139 (t) REVERT: B 182 TYR cc_start: 0.6879 (t80) cc_final: 0.6017 (t80) REVERT: B 679 MET cc_start: 0.5128 (mmm) cc_final: 0.4561 (tmm) REVERT: B 835 MET cc_start: 0.7232 (mmt) cc_final: 0.6782 (mmm) REVERT: B 892 GLU cc_start: 0.5779 (tt0) cc_final: 0.5396 (tt0) REVERT: B 916 THR cc_start: 0.7895 (p) cc_final: 0.7642 (t) REVERT: B 1104 LYS cc_start: 0.7762 (mmpt) cc_final: 0.7509 (tppt) REVERT: B 1105 MET cc_start: 0.6233 (mtt) cc_final: 0.5475 (mtt) REVERT: B 1114 TYR cc_start: 0.5840 (t80) cc_final: 0.5563 (t80) REVERT: C 85 MET cc_start: 0.1942 (tpt) cc_final: 0.0332 (ttm) REVERT: C 135 TRP cc_start: 0.7342 (m-10) cc_final: 0.7096 (m-90) REVERT: C 514 ARG cc_start: 0.6094 (mtt180) cc_final: 0.5619 (ttm-80) REVERT: C 602 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7520 (tp-100) REVERT: C 753 GLN cc_start: 0.7214 (mt0) cc_final: 0.6859 (mt0) REVERT: C 1166 MET cc_start: 0.0480 (mmm) cc_final: -0.0337 (ptm) REVERT: C 1304 THR cc_start: 0.7384 (p) cc_final: 0.7123 (t) REVERT: D 182 TYR cc_start: 0.7085 (t80) cc_final: 0.6170 (t80) REVERT: D 449 MET cc_start: 0.0909 (mmm) cc_final: 0.0638 (mmp) REVERT: D 606 LEU cc_start: 0.6428 (mm) cc_final: 0.6205 (mm) REVERT: D 679 MET cc_start: 0.5392 (mmm) cc_final: 0.4718 (tmm) REVERT: D 973 ASN cc_start: 0.8064 (m-40) cc_final: 0.7693 (m-40) REVERT: D 1104 LYS cc_start: 0.7624 (mmpt) cc_final: 0.7409 (tppt) REVERT: D 1114 TYR cc_start: 0.6149 (t80) cc_final: 0.5903 (t80) outliers start: 1 outliers final: 0 residues processed: 669 average time/residue: 0.2097 time to fit residues: 230.7996 Evaluate side-chains 491 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 37 optimal weight: 0.1980 chunk 346 optimal weight: 10.0000 chunk 177 optimal weight: 0.0270 chunk 213 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 332 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 401 optimal weight: 7.9990 overall best weight: 3.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** A1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS B 22 HIS ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS B 708 GLN B 759 GLN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 HIS ** C1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS D 708 GLN D 759 GLN D 803 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.181187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.153221 restraints weight = 71771.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.151747 restraints weight = 95306.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.153475 restraints weight = 80740.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.153650 restraints weight = 59789.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.155112 restraints weight = 49425.634| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 36050 Z= 0.174 Angle : 0.667 7.888 48828 Z= 0.347 Chirality : 0.046 0.146 5596 Planarity : 0.005 0.049 6294 Dihedral : 5.838 27.958 4816 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.54 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.11), residues: 4454 helix: -1.84 (0.15), residues: 1050 sheet: -1.82 (0.16), residues: 984 loop : -2.87 (0.11), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 178 TYR 0.025 0.002 TYR D1048 PHE 0.023 0.002 PHE C 133 TRP 0.030 0.003 TRP C 726 HIS 0.010 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00396 (36046) covalent geometry : angle 0.66706 (48820) SS BOND : bond 0.00447 ( 4) SS BOND : angle 1.22693 ( 8) hydrogen bonds : bond 0.03648 ( 883) hydrogen bonds : angle 6.43911 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.1623 (tpt) cc_final: -0.0012 (ttm) REVERT: A 427 MET cc_start: 0.5437 (tpt) cc_final: 0.4958 (tpp) REVERT: A 572 MET cc_start: 0.7038 (ptp) cc_final: 0.6737 (ptp) REVERT: A 753 GLN cc_start: 0.7495 (mt0) cc_final: 0.7025 (mt0) REVERT: A 773 GLN cc_start: 0.7584 (pp30) cc_final: 0.7220 (mp10) REVERT: A 845 PHE cc_start: 0.4042 (p90) cc_final: 0.3810 (p90) REVERT: A 1166 MET cc_start: 0.0812 (mmm) cc_final: -0.0249 (ptm) REVERT: A 1172 MET cc_start: 0.6661 (tpp) cc_final: 0.6407 (tpp) REVERT: A 1288 LEU cc_start: 0.8338 (mp) cc_final: 0.8017 (tt) REVERT: B 131 ILE cc_start: 0.9021 (mt) cc_final: 0.8799 (mm) REVERT: B 182 TYR cc_start: 0.6730 (t80) cc_final: 0.5857 (t80) REVERT: B 835 MET cc_start: 0.7359 (mmt) cc_final: 0.6727 (mmm) REVERT: B 1104 LYS cc_start: 0.7890 (mmpt) cc_final: 0.7535 (tppt) REVERT: B 1105 MET cc_start: 0.6384 (mtt) cc_final: 0.5697 (mtt) REVERT: B 1114 TYR cc_start: 0.5851 (t80) cc_final: 0.5083 (t80) REVERT: C 85 MET cc_start: 0.1703 (tpt) cc_final: 0.0117 (ttm) REVERT: C 427 MET cc_start: 0.5461 (tpt) cc_final: 0.5041 (tpp) REVERT: C 572 MET cc_start: 0.7008 (ptp) cc_final: 0.6717 (ptp) REVERT: C 773 GLN cc_start: 0.7683 (pp30) cc_final: 0.7220 (mp10) REVERT: C 845 PHE cc_start: 0.3945 (p90) cc_final: 0.3679 (p90) REVERT: C 1166 MET cc_start: 0.0807 (mmm) cc_final: -0.0268 (ptm) REVERT: C 1172 MET cc_start: 0.6619 (tpp) cc_final: 0.6385 (tpp) REVERT: D 182 TYR cc_start: 0.7029 (t80) cc_final: 0.6246 (t80) REVERT: D 606 LEU cc_start: 0.6360 (mm) cc_final: 0.6135 (mm) REVERT: D 679 MET cc_start: 0.5556 (mmm) cc_final: 0.4611 (tmm) REVERT: D 973 ASN cc_start: 0.7999 (m-40) cc_final: 0.7478 (m-40) REVERT: D 1104 LYS cc_start: 0.7739 (mmpt) cc_final: 0.7431 (tppt) outliers start: 0 outliers final: 0 residues processed: 652 average time/residue: 0.2027 time to fit residues: 216.3110 Evaluate side-chains 476 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 417 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 419 optimal weight: 6.9990 chunk 379 optimal weight: 10.0000 chunk 435 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 330 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 378 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 609 ASN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 708 GLN B 759 GLN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 GLN D 536 HIS D 708 GLN D 759 GLN D 964 ASN D1077 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.183641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.156045 restraints weight = 72121.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.154585 restraints weight = 88355.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.156422 restraints weight = 72556.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.156508 restraints weight = 55861.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.156838 restraints weight = 49647.527| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36050 Z= 0.122 Angle : 0.616 7.918 48828 Z= 0.317 Chirality : 0.045 0.189 5596 Planarity : 0.004 0.047 6294 Dihedral : 5.505 26.562 4816 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.96 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.12), residues: 4454 helix: -1.51 (0.15), residues: 1052 sheet: -1.78 (0.16), residues: 1034 loop : -2.77 (0.11), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 369 TYR 0.024 0.001 TYR B1048 PHE 0.026 0.002 PHE A 133 TRP 0.031 0.002 TRP A 610 HIS 0.004 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00277 (36046) covalent geometry : angle 0.61556 (48820) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.99401 ( 8) hydrogen bonds : bond 0.03194 ( 883) hydrogen bonds : angle 5.94755 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.1928 (tpt) cc_final: 0.0465 (ttm) REVERT: A 348 MET cc_start: 0.6437 (mtp) cc_final: 0.6200 (mtp) REVERT: A 402 GLU cc_start: 0.6587 (mt-10) cc_final: 0.5386 (tm-30) REVERT: A 427 MET cc_start: 0.5526 (tpt) cc_final: 0.5139 (tpp) REVERT: A 572 MET cc_start: 0.7104 (ptp) cc_final: 0.6767 (ptp) REVERT: A 753 GLN cc_start: 0.7545 (mt0) cc_final: 0.7255 (tp-100) REVERT: A 773 GLN cc_start: 0.7551 (pp30) cc_final: 0.7091 (mp10) REVERT: A 845 PHE cc_start: 0.4075 (p90) cc_final: 0.3823 (p90) REVERT: A 1105 GLU cc_start: 0.7357 (pp20) cc_final: 0.7060 (pp20) REVERT: A 1166 MET cc_start: 0.0803 (mmm) cc_final: -0.0296 (ptm) REVERT: A 1172 MET cc_start: 0.6435 (tpp) cc_final: 0.5974 (tpp) REVERT: A 1244 TRP cc_start: 0.5599 (m100) cc_final: 0.5350 (m100) REVERT: A 1288 LEU cc_start: 0.8497 (mp) cc_final: 0.8072 (tt) REVERT: A 1304 THR cc_start: 0.7488 (p) cc_final: 0.7211 (t) REVERT: A 1330 PHE cc_start: 0.2971 (m-80) cc_final: 0.2562 (m-80) REVERT: A 1345 ILE cc_start: 0.5995 (mp) cc_final: 0.5461 (mt) REVERT: B 133 LEU cc_start: 0.7564 (mt) cc_final: 0.7289 (mt) REVERT: B 182 TYR cc_start: 0.6847 (t80) cc_final: 0.5913 (t80) REVERT: B 893 TRP cc_start: 0.6998 (t-100) cc_final: 0.5438 (t-100) REVERT: B 1014 MET cc_start: 0.3534 (tpp) cc_final: 0.2662 (tpp) REVERT: B 1065 VAL cc_start: 0.5307 (t) cc_final: 0.4872 (t) REVERT: B 1104 LYS cc_start: 0.7892 (mmpt) cc_final: 0.7562 (tppt) REVERT: B 1105 MET cc_start: 0.6314 (mtt) cc_final: 0.5765 (mtt) REVERT: C 85 MET cc_start: 0.1879 (tpt) cc_final: 0.0406 (ttm) REVERT: C 183 GLN cc_start: 0.6087 (mt0) cc_final: 0.5814 (mt0) REVERT: C 348 MET cc_start: 0.6379 (mtp) cc_final: 0.6137 (mtp) REVERT: C 357 MET cc_start: 0.5879 (mmm) cc_final: 0.5512 (mmm) REVERT: C 399 LYS cc_start: 0.6861 (tptp) cc_final: 0.6644 (tptp) REVERT: C 402 GLU cc_start: 0.6595 (mt-10) cc_final: 0.5403 (tm-30) REVERT: C 427 MET cc_start: 0.5571 (tpt) cc_final: 0.5232 (tpp) REVERT: C 572 MET cc_start: 0.7244 (ptp) cc_final: 0.6742 (ptp) REVERT: C 753 GLN cc_start: 0.7187 (tp-100) cc_final: 0.6452 (mt0) REVERT: C 757 LEU cc_start: 0.8173 (mt) cc_final: 0.7882 (mt) REVERT: C 773 GLN cc_start: 0.7688 (pp30) cc_final: 0.7164 (mp10) REVERT: C 845 PHE cc_start: 0.3979 (p90) cc_final: 0.3749 (p90) REVERT: C 1166 MET cc_start: 0.0759 (mmm) cc_final: -0.0315 (ptm) REVERT: C 1172 MET cc_start: 0.6541 (tpp) cc_final: 0.6081 (tpp) REVERT: C 1304 THR cc_start: 0.7427 (p) cc_final: 0.7189 (t) REVERT: C 1330 PHE cc_start: 0.3077 (m-80) cc_final: 0.2623 (m-80) REVERT: C 1345 ILE cc_start: 0.5933 (mp) cc_final: 0.5443 (mt) REVERT: D 182 TYR cc_start: 0.6999 (t80) cc_final: 0.5934 (t80) REVERT: D 606 LEU cc_start: 0.6398 (mm) cc_final: 0.6165 (mm) REVERT: D 679 MET cc_start: 0.5371 (mmm) cc_final: 0.4597 (tmm) REVERT: D 1014 MET cc_start: 0.5159 (tpt) cc_final: 0.4698 (tpt) outliers start: 0 outliers final: 0 residues processed: 647 average time/residue: 0.2040 time to fit residues: 215.8979 Evaluate side-chains 496 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 221 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 360 optimal weight: 0.8980 chunk 384 optimal weight: 0.4980 chunk 165 optimal weight: 10.0000 chunk 333 optimal weight: 0.6980 chunk 172 optimal weight: 30.0000 chunk 80 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** A1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 708 GLN B 810 ASN C 519 HIS ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 HIS ** C1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 708 GLN D 789 HIS D 803 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.185624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.158597 restraints weight = 72151.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.157727 restraints weight = 81972.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.159635 restraints weight = 67023.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.159379 restraints weight = 44316.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.159684 restraints weight = 41890.017| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36050 Z= 0.105 Angle : 0.595 10.711 48828 Z= 0.304 Chirality : 0.044 0.168 5596 Planarity : 0.004 0.048 6294 Dihedral : 5.198 26.592 4816 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.06 % Favored : 91.92 % Rotamer: Outliers : 0.05 % Allowed : 1.85 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.12), residues: 4454 helix: -1.26 (0.15), residues: 1058 sheet: -1.62 (0.15), residues: 1080 loop : -2.64 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1138 TYR 0.021 0.001 TYR B1048 PHE 0.020 0.001 PHE A 133 TRP 0.050 0.002 TRP C 135 HIS 0.012 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00232 (36046) covalent geometry : angle 0.59452 (48820) SS BOND : bond 0.00069 ( 4) SS BOND : angle 0.74481 ( 8) hydrogen bonds : bond 0.02991 ( 883) hydrogen bonds : angle 5.67697 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 661 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.1485 (tpt) cc_final: 0.0137 (ttm) REVERT: A 357 MET cc_start: 0.5529 (tpt) cc_final: 0.4610 (mmm) REVERT: A 427 MET cc_start: 0.5307 (tpt) cc_final: 0.5012 (tpp) REVERT: A 572 MET cc_start: 0.7248 (ptp) cc_final: 0.6835 (ptp) REVERT: A 753 GLN cc_start: 0.7506 (mt0) cc_final: 0.6956 (tp-100) REVERT: A 773 GLN cc_start: 0.7569 (pp30) cc_final: 0.7141 (mp10) REVERT: A 845 PHE cc_start: 0.4069 (p90) cc_final: 0.3780 (p90) REVERT: A 1014 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 1105 GLU cc_start: 0.7271 (pp20) cc_final: 0.7045 (pp20) REVERT: A 1166 MET cc_start: 0.0836 (mmm) cc_final: -0.0314 (ptm) REVERT: A 1172 MET cc_start: 0.6222 (tpp) cc_final: 0.5786 (tpp) REVERT: A 1288 LEU cc_start: 0.8416 (mp) cc_final: 0.7956 (tt) REVERT: A 1304 THR cc_start: 0.7365 (p) cc_final: 0.7080 (t) REVERT: A 1330 PHE cc_start: 0.2797 (m-80) cc_final: 0.2376 (m-80) REVERT: A 1345 ILE cc_start: 0.5722 (mp) cc_final: 0.5196 (mt) REVERT: B 133 LEU cc_start: 0.7618 (mt) cc_final: 0.7374 (mt) REVERT: B 182 TYR cc_start: 0.6799 (t80) cc_final: 0.5921 (t80) REVERT: B 893 TRP cc_start: 0.6902 (t-100) cc_final: 0.5374 (t-100) REVERT: B 1014 MET cc_start: 0.3473 (tpp) cc_final: 0.2744 (tpp) REVERT: B 1104 LYS cc_start: 0.7767 (mmpt) cc_final: 0.7542 (tppt) REVERT: B 1105 MET cc_start: 0.6248 (mtt) cc_final: 0.5814 (mtt) REVERT: C 85 MET cc_start: 0.1476 (tpt) cc_final: 0.0183 (ttm) REVERT: C 357 MET cc_start: 0.5802 (mmm) cc_final: 0.5429 (mmm) REVERT: C 427 MET cc_start: 0.5382 (tpt) cc_final: 0.5075 (tpp) REVERT: C 572 MET cc_start: 0.7285 (ptp) cc_final: 0.6818 (ptp) REVERT: C 773 GLN cc_start: 0.7695 (pp30) cc_final: 0.7130 (mp10) REVERT: C 845 PHE cc_start: 0.4133 (p90) cc_final: 0.3834 (p90) REVERT: C 1105 GLU cc_start: 0.7325 (pp20) cc_final: 0.7058 (pp20) REVERT: C 1166 MET cc_start: 0.0782 (mmm) cc_final: -0.0308 (ptm) REVERT: C 1172 MET cc_start: 0.6323 (tpp) cc_final: 0.5888 (tpp) REVERT: C 1330 PHE cc_start: 0.2917 (m-80) cc_final: 0.2419 (m-80) REVERT: C 1345 ILE cc_start: 0.5741 (mp) cc_final: 0.5235 (mt) REVERT: D 182 TYR cc_start: 0.7005 (t80) cc_final: 0.5998 (t80) REVERT: D 606 LEU cc_start: 0.6518 (mm) cc_final: 0.6297 (mm) REVERT: D 679 MET cc_start: 0.5369 (mmm) cc_final: 0.4533 (tmm) REVERT: D 989 ARG cc_start: 0.7553 (ptm160) cc_final: 0.7343 (ptm-80) REVERT: D 1014 MET cc_start: 0.4783 (tpt) cc_final: 0.4407 (tpt) REVERT: D 1104 LYS cc_start: 0.7673 (mmpt) cc_final: 0.7446 (tppt) outliers start: 2 outliers final: 0 residues processed: 663 average time/residue: 0.1917 time to fit residues: 211.1060 Evaluate side-chains 512 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 157 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 213 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 427 optimal weight: 0.6980 chunk 417 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 708 GLN B 789 HIS B 803 HIS C 183 GLN C 788 GLN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 HIS ** C1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 708 GLN D 789 HIS D 803 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.186550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.159898 restraints weight = 72895.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.158706 restraints weight = 83608.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.160780 restraints weight = 71943.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.160885 restraints weight = 48770.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.161267 restraints weight = 44483.002| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36050 Z= 0.104 Angle : 0.595 8.686 48828 Z= 0.302 Chirality : 0.044 0.170 5596 Planarity : 0.004 0.048 6294 Dihedral : 5.018 26.271 4816 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.99 % Favored : 91.96 % Rotamer: Outliers : 0.05 % Allowed : 1.22 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.12), residues: 4454 helix: -1.05 (0.16), residues: 1060 sheet: -1.50 (0.16), residues: 1006 loop : -2.58 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 616 TYR 0.017 0.001 TYR B1048 PHE 0.020 0.001 PHE A 133 TRP 0.038 0.002 TRP C 135 HIS 0.008 0.001 HIS D 789 Details of bonding type rmsd covalent geometry : bond 0.00232 (36046) covalent geometry : angle 0.59546 (48820) SS BOND : bond 0.00063 ( 4) SS BOND : angle 0.67900 ( 8) hydrogen bonds : bond 0.02852 ( 883) hydrogen bonds : angle 5.45165 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 650 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.1509 (tpt) cc_final: 0.0178 (ttm) REVERT: A 357 MET cc_start: 0.5541 (tpt) cc_final: 0.5146 (mmm) REVERT: A 427 MET cc_start: 0.5232 (tpt) cc_final: 0.4934 (tpp) REVERT: A 572 MET cc_start: 0.7320 (ptp) cc_final: 0.6928 (ptp) REVERT: A 726 TRP cc_start: 0.7438 (m-10) cc_final: 0.6955 (m-10) REVERT: A 753 GLN cc_start: 0.7438 (mt0) cc_final: 0.7086 (tp-100) REVERT: A 773 GLN cc_start: 0.7539 (pp30) cc_final: 0.7058 (mp10) REVERT: A 845 PHE cc_start: 0.4231 (p90) cc_final: 0.3993 (p90) REVERT: A 1014 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7621 (mm-30) REVERT: A 1105 GLU cc_start: 0.7373 (pp20) cc_final: 0.7085 (pp20) REVERT: A 1166 MET cc_start: 0.0935 (mmm) cc_final: -0.0296 (ptm) REVERT: A 1172 MET cc_start: 0.6265 (tpp) cc_final: 0.5861 (tpp) REVERT: A 1288 LEU cc_start: 0.8355 (mp) cc_final: 0.8050 (tt) REVERT: A 1294 LEU cc_start: 0.7581 (mt) cc_final: 0.7237 (mt) REVERT: A 1304 THR cc_start: 0.7358 (p) cc_final: 0.7102 (t) REVERT: A 1330 PHE cc_start: 0.2782 (m-80) cc_final: 0.2230 (m-80) REVERT: A 1345 ILE cc_start: 0.5839 (mp) cc_final: 0.5319 (mt) REVERT: B 102 THR cc_start: 0.7498 (m) cc_final: 0.7086 (p) REVERT: B 133 LEU cc_start: 0.7657 (mt) cc_final: 0.7411 (mt) REVERT: B 182 TYR cc_start: 0.6775 (t80) cc_final: 0.5849 (t80) REVERT: B 213 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7947 (tp30) REVERT: B 892 GLU cc_start: 0.6270 (tt0) cc_final: 0.5655 (tt0) REVERT: B 893 TRP cc_start: 0.6802 (t-100) cc_final: 0.5530 (t-100) REVERT: B 993 GLN cc_start: 0.7030 (mm110) cc_final: 0.6323 (mt0) REVERT: B 1014 MET cc_start: 0.3347 (tpp) cc_final: 0.2928 (tpp) REVERT: C 85 MET cc_start: 0.1498 (tpt) cc_final: 0.0240 (ttm) REVERT: C 357 MET cc_start: 0.5792 (mmm) cc_final: 0.5496 (mmm) REVERT: C 427 MET cc_start: 0.5351 (tpt) cc_final: 0.5034 (tpp) REVERT: C 436 ASN cc_start: 0.5688 (p0) cc_final: 0.5487 (m-40) REVERT: C 572 MET cc_start: 0.7329 (ptp) cc_final: 0.6885 (ptp) REVERT: C 753 GLN cc_start: 0.7068 (tp-100) cc_final: 0.6529 (mt0) REVERT: C 773 GLN cc_start: 0.7601 (pp30) cc_final: 0.7169 (mp10) REVERT: C 845 PHE cc_start: 0.4096 (p90) cc_final: 0.3743 (p90) REVERT: C 1166 MET cc_start: 0.0883 (mmm) cc_final: -0.0271 (ptm) REVERT: C 1172 MET cc_start: 0.6319 (tpp) cc_final: 0.5998 (tpp) REVERT: C 1330 PHE cc_start: 0.2858 (m-80) cc_final: 0.2273 (m-80) REVERT: C 1345 ILE cc_start: 0.5865 (mp) cc_final: 0.5370 (mt) REVERT: D 182 TYR cc_start: 0.7041 (t80) cc_final: 0.6036 (t80) REVERT: D 679 MET cc_start: 0.5040 (mmm) cc_final: 0.4442 (tmm) REVERT: D 973 ASN cc_start: 0.7896 (m-40) cc_final: 0.7652 (m-40) REVERT: D 989 ARG cc_start: 0.7521 (ptm160) cc_final: 0.7281 (ptm-80) REVERT: D 1014 MET cc_start: 0.4752 (tpt) cc_final: 0.4418 (tpt) REVERT: D 1104 LYS cc_start: 0.7633 (mmpt) cc_final: 0.7421 (tppt) outliers start: 2 outliers final: 0 residues processed: 652 average time/residue: 0.1960 time to fit residues: 209.9204 Evaluate side-chains 520 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 79 optimal weight: 10.0000 chunk 431 optimal weight: 2.9990 chunk 173 optimal weight: 0.4980 chunk 333 optimal weight: 6.9990 chunk 380 optimal weight: 10.0000 chunk 433 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 394 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 237 optimal weight: 0.0030 chunk 32 optimal weight: 0.8980 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** A1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 536 HIS B 708 GLN B 796 GLN B 803 HIS ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 HIS ** C1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1371 ASN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 708 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.186217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.158919 restraints weight = 72495.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.157978 restraints weight = 84618.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.159463 restraints weight = 68454.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.160359 restraints weight = 49145.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.160399 restraints weight = 42687.750| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36050 Z= 0.107 Angle : 0.594 8.217 48828 Z= 0.302 Chirality : 0.044 0.161 5596 Planarity : 0.004 0.061 6294 Dihedral : 4.978 26.597 4816 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.46 % Favored : 91.49 % Rotamer: Outliers : 0.08 % Allowed : 0.68 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.12), residues: 4454 helix: -0.96 (0.16), residues: 1076 sheet: -1.44 (0.16), residues: 1032 loop : -2.49 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1138 TYR 0.015 0.001 TYR B1048 PHE 0.022 0.001 PHE A1355 TRP 0.076 0.002 TRP C 135 HIS 0.013 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00243 (36046) covalent geometry : angle 0.59436 (48820) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.67922 ( 8) hydrogen bonds : bond 0.02810 ( 883) hydrogen bonds : angle 5.35096 ( 2352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 633 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.1522 (tpt) cc_final: 0.0136 (ttm) REVERT: A 357 MET cc_start: 0.5582 (tpt) cc_final: 0.5299 (tpt) REVERT: A 427 MET cc_start: 0.5148 (tpt) cc_final: 0.4845 (tpp) REVERT: A 572 MET cc_start: 0.7342 (ptp) cc_final: 0.7054 (ptp) REVERT: A 726 TRP cc_start: 0.7315 (m-10) cc_final: 0.6217 (m-10) REVERT: A 753 GLN cc_start: 0.7354 (mt0) cc_final: 0.7032 (tp-100) REVERT: A 773 GLN cc_start: 0.7564 (pp30) cc_final: 0.6987 (mp10) REVERT: A 815 ARG cc_start: 0.6780 (tpm170) cc_final: 0.6515 (tpm170) REVERT: A 845 PHE cc_start: 0.4165 (p90) cc_final: 0.3835 (p90) REVERT: A 1014 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 1166 MET cc_start: 0.0904 (mmm) cc_final: -0.0332 (ptm) REVERT: A 1172 MET cc_start: 0.6264 (tpp) cc_final: 0.5893 (tpp) REVERT: A 1288 LEU cc_start: 0.8283 (mp) cc_final: 0.7844 (tt) REVERT: A 1294 LEU cc_start: 0.7454 (mt) cc_final: 0.7136 (mt) REVERT: A 1304 THR cc_start: 0.7325 (p) cc_final: 0.7038 (t) REVERT: A 1345 ILE cc_start: 0.5836 (mp) cc_final: 0.5342 (mt) REVERT: B 102 THR cc_start: 0.7501 (m) cc_final: 0.7083 (p) REVERT: B 182 TYR cc_start: 0.6985 (t80) cc_final: 0.6040 (t80) REVERT: B 893 TRP cc_start: 0.6675 (t-100) cc_final: 0.5184 (t-100) REVERT: B 993 GLN cc_start: 0.6979 (mm110) cc_final: 0.6319 (mt0) REVERT: B 1014 MET cc_start: 0.3297 (tpp) cc_final: 0.2603 (tpp) REVERT: B 1104 LYS cc_start: 0.7705 (mmpt) cc_final: 0.7474 (tppt) REVERT: C 85 MET cc_start: 0.1518 (tpt) cc_final: 0.0213 (ttm) REVERT: C 427 MET cc_start: 0.5286 (tpt) cc_final: 0.5020 (tpp) REVERT: C 572 MET cc_start: 0.7397 (ptp) cc_final: 0.7033 (ptp) REVERT: C 773 GLN cc_start: 0.7649 (pp30) cc_final: 0.7107 (mp10) REVERT: C 845 PHE cc_start: 0.4182 (p90) cc_final: 0.3762 (p90) REVERT: C 1105 GLU cc_start: 0.7224 (pp20) cc_final: 0.7010 (pp20) REVERT: C 1166 MET cc_start: 0.0857 (mmm) cc_final: -0.0352 (ptm) REVERT: C 1172 MET cc_start: 0.6350 (tpp) cc_final: 0.5991 (tpp) REVERT: C 1205 ILE cc_start: 0.6034 (mm) cc_final: 0.5805 (mm) REVERT: C 1294 LEU cc_start: 0.7632 (mt) cc_final: 0.7192 (mt) REVERT: C 1345 ILE cc_start: 0.5772 (mp) cc_final: 0.5266 (mt) REVERT: D 182 TYR cc_start: 0.7130 (t80) cc_final: 0.6128 (t80) REVERT: D 606 LEU cc_start: 0.6545 (mm) cc_final: 0.6344 (mm) REVERT: D 679 MET cc_start: 0.4922 (mmm) cc_final: 0.4557 (tmm) REVERT: D 719 GLU cc_start: 0.6117 (tt0) cc_final: 0.5295 (mt-10) REVERT: D 757 SER cc_start: 0.8562 (p) cc_final: 0.8261 (p) REVERT: D 989 ARG cc_start: 0.7461 (ptm160) cc_final: 0.7205 (ptm-80) REVERT: D 1105 MET cc_start: 0.6111 (mtt) cc_final: 0.5563 (mtt) outliers start: 3 outliers final: 0 residues processed: 636 average time/residue: 0.1944 time to fit residues: 204.4035 Evaluate side-chains 505 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 197 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 101 optimal weight: 0.4980 chunk 330 optimal weight: 0.9980 chunk 302 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 271 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** A1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 528 GLN B 708 GLN B 796 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 HIS ** C1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1371 ASN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 708 GLN D 964 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.187262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.160493 restraints weight = 72080.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.159477 restraints weight = 83940.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.161699 restraints weight = 69119.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.161629 restraints weight = 45144.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.162061 restraints weight = 41945.008| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36050 Z= 0.101 Angle : 0.600 12.401 48828 Z= 0.300 Chirality : 0.044 0.247 5596 Planarity : 0.004 0.049 6294 Dihedral : 4.850 26.096 4816 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.84 % Favored : 92.12 % Rotamer: Outliers : 0.08 % Allowed : 0.51 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.12), residues: 4454 helix: -0.91 (0.16), residues: 1092 sheet: -1.33 (0.16), residues: 1028 loop : -2.45 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1138 TYR 0.015 0.001 TYR C1223 PHE 0.030 0.001 PHE D1097 TRP 0.080 0.002 TRP C 135 HIS 0.012 0.001 HIS D 789 Details of bonding type rmsd covalent geometry : bond 0.00226 (36046) covalent geometry : angle 0.60024 (48820) SS BOND : bond 0.00039 ( 4) SS BOND : angle 0.61237 ( 8) hydrogen bonds : bond 0.02662 ( 883) hydrogen bonds : angle 5.23571 ( 2352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 649 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.1447 (tpt) cc_final: 0.0116 (ttm) REVERT: A 427 MET cc_start: 0.4916 (tpt) cc_final: 0.4532 (tpp) REVERT: A 572 MET cc_start: 0.7433 (ptp) cc_final: 0.7115 (ptp) REVERT: A 612 THR cc_start: 0.7377 (m) cc_final: 0.7137 (m) REVERT: A 726 TRP cc_start: 0.7215 (m-10) cc_final: 0.6163 (m-10) REVERT: A 753 GLN cc_start: 0.7338 (mt0) cc_final: 0.6913 (tp-100) REVERT: A 773 GLN cc_start: 0.7673 (pp30) cc_final: 0.7121 (mp10) REVERT: A 815 ARG cc_start: 0.6776 (tpm170) cc_final: 0.6536 (tpm170) REVERT: A 845 PHE cc_start: 0.4089 (p90) cc_final: 0.3727 (p90) REVERT: A 1014 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 1166 MET cc_start: 0.1021 (mmm) cc_final: -0.0463 (ptm) REVERT: A 1172 MET cc_start: 0.6116 (tpp) cc_final: 0.5778 (tpp) REVERT: A 1186 LYS cc_start: 0.6142 (mmmt) cc_final: 0.5791 (mmmm) REVERT: A 1288 LEU cc_start: 0.8334 (mp) cc_final: 0.7897 (tt) REVERT: A 1294 LEU cc_start: 0.7479 (mt) cc_final: 0.7182 (mt) REVERT: A 1304 THR cc_start: 0.7324 (p) cc_final: 0.7036 (t) REVERT: B 102 THR cc_start: 0.7470 (m) cc_final: 0.7048 (p) REVERT: B 182 TYR cc_start: 0.6897 (t80) cc_final: 0.5939 (t80) REVERT: B 893 TRP cc_start: 0.6575 (t-100) cc_final: 0.5255 (t-100) REVERT: B 993 GLN cc_start: 0.7036 (mm110) cc_final: 0.6298 (mt0) REVERT: B 1014 MET cc_start: 0.3455 (tpp) cc_final: 0.3074 (tpp) REVERT: C 85 MET cc_start: 0.1415 (tpt) cc_final: 0.0118 (ttm) REVERT: C 427 MET cc_start: 0.5078 (tpt) cc_final: 0.4800 (tpp) REVERT: C 572 MET cc_start: 0.7431 (ptp) cc_final: 0.7079 (ptp) REVERT: C 612 THR cc_start: 0.7384 (m) cc_final: 0.7182 (m) REVERT: C 726 TRP cc_start: 0.7374 (m-10) cc_final: 0.6840 (m-10) REVERT: C 773 GLN cc_start: 0.7755 (pp30) cc_final: 0.7085 (mp10) REVERT: C 845 PHE cc_start: 0.4116 (p90) cc_final: 0.3760 (p90) REVERT: C 1166 MET cc_start: 0.0971 (mmm) cc_final: -0.0470 (ptm) REVERT: C 1172 MET cc_start: 0.6219 (tpp) cc_final: 0.5872 (tpp) REVERT: C 1186 LYS cc_start: 0.6294 (mmmt) cc_final: 0.5937 (mmmm) REVERT: C 1205 ILE cc_start: 0.5744 (mm) cc_final: 0.5395 (mm) REVERT: C 1294 LEU cc_start: 0.7618 (mt) cc_final: 0.7265 (mt) REVERT: D 102 THR cc_start: 0.7468 (m) cc_final: 0.7009 (p) REVERT: D 182 TYR cc_start: 0.7086 (t80) cc_final: 0.6092 (t80) REVERT: D 606 LEU cc_start: 0.6665 (mm) cc_final: 0.6464 (mm) REVERT: D 719 GLU cc_start: 0.6252 (tt0) cc_final: 0.5424 (mt-10) REVERT: D 757 SER cc_start: 0.8596 (p) cc_final: 0.8293 (p) REVERT: D 770 LEU cc_start: 0.6749 (pt) cc_final: 0.6215 (pp) REVERT: D 989 ARG cc_start: 0.7503 (ptm160) cc_final: 0.7274 (ptm-80) REVERT: D 1105 MET cc_start: 0.6069 (mtt) cc_final: 0.5765 (mtp) outliers start: 3 outliers final: 0 residues processed: 652 average time/residue: 0.2012 time to fit residues: 215.6538 Evaluate side-chains 497 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 30 optimal weight: 7.9990 chunk 375 optimal weight: 20.0000 chunk 264 optimal weight: 0.9980 chunk 369 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 421 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 63 optimal weight: 0.0970 overall best weight: 2.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** A1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 355 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 708 GLN ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 HIS ** C1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1371 ASN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 708 GLN D 759 GLN ** D 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.183442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.156576 restraints weight = 72737.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.155373 restraints weight = 82534.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.157450 restraints weight = 68766.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.157423 restraints weight = 45299.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.157729 restraints weight = 41826.283| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36050 Z= 0.141 Angle : 0.636 9.587 48828 Z= 0.324 Chirality : 0.046 0.257 5596 Planarity : 0.004 0.048 6294 Dihedral : 5.032 25.459 4816 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.12 % Favored : 90.84 % Rotamer: Outliers : 0.08 % Allowed : 0.41 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.12), residues: 4454 helix: -0.93 (0.16), residues: 1086 sheet: -1.33 (0.16), residues: 1018 loop : -2.50 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 616 TYR 0.016 0.001 TYR B1048 PHE 0.021 0.002 PHE A1355 TRP 0.019 0.002 TRP A 610 HIS 0.012 0.001 HIS D 789 Details of bonding type rmsd covalent geometry : bond 0.00325 (36046) covalent geometry : angle 0.63634 (48820) SS BOND : bond 0.00284 ( 4) SS BOND : angle 0.79738 ( 8) hydrogen bonds : bond 0.02977 ( 883) hydrogen bonds : angle 5.47010 ( 2352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 619 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.1426 (tpt) cc_final: -0.0021 (ttm) REVERT: A 183 GLN cc_start: 0.6017 (mt0) cc_final: 0.5761 (mt0) REVERT: A 427 MET cc_start: 0.5061 (tpt) cc_final: 0.4732 (tpp) REVERT: A 568 ILE cc_start: 0.7342 (tp) cc_final: 0.7140 (tp) REVERT: A 572 MET cc_start: 0.7613 (ptp) cc_final: 0.7323 (ptp) REVERT: A 753 GLN cc_start: 0.7438 (mt0) cc_final: 0.6976 (tp-100) REVERT: A 773 GLN cc_start: 0.7596 (pp30) cc_final: 0.6898 (mp10) REVERT: A 845 PHE cc_start: 0.4160 (p90) cc_final: 0.3712 (p90) REVERT: A 1166 MET cc_start: 0.1286 (mmm) cc_final: -0.0233 (ptm) REVERT: A 1172 MET cc_start: 0.6333 (tpp) cc_final: 0.5984 (tpp) REVERT: A 1186 LYS cc_start: 0.6300 (mmmt) cc_final: 0.6010 (mmmm) REVERT: A 1288 LEU cc_start: 0.8389 (mp) cc_final: 0.7953 (tt) REVERT: A 1294 LEU cc_start: 0.7774 (mt) cc_final: 0.7377 (mt) REVERT: A 1304 THR cc_start: 0.7482 (p) cc_final: 0.7209 (t) REVERT: A 1345 ILE cc_start: 0.5995 (mp) cc_final: 0.5305 (mt) REVERT: B 102 THR cc_start: 0.7541 (m) cc_final: 0.7069 (p) REVERT: B 182 TYR cc_start: 0.6929 (t80) cc_final: 0.6030 (t80) REVERT: B 893 TRP cc_start: 0.6262 (t-100) cc_final: 0.4876 (t-100) REVERT: B 925 ASP cc_start: 0.7541 (t0) cc_final: 0.6785 (p0) REVERT: B 1014 MET cc_start: 0.3428 (tpp) cc_final: 0.2843 (tpp) REVERT: C 85 MET cc_start: 0.1530 (tpt) cc_final: 0.0129 (ttm) REVERT: C 427 MET cc_start: 0.5195 (tpt) cc_final: 0.4898 (tpp) REVERT: C 572 MET cc_start: 0.7656 (ptp) cc_final: 0.7315 (ptp) REVERT: C 773 GLN cc_start: 0.7646 (pp30) cc_final: 0.6843 (mp10) REVERT: C 845 PHE cc_start: 0.4154 (p90) cc_final: 0.3610 (p90) REVERT: C 1166 MET cc_start: 0.1256 (mmm) cc_final: -0.0216 (ptm) REVERT: C 1172 MET cc_start: 0.6492 (tpp) cc_final: 0.6145 (tpp) REVERT: C 1186 LYS cc_start: 0.6397 (mmmt) cc_final: 0.6141 (mmmm) REVERT: C 1205 ILE cc_start: 0.5723 (mm) cc_final: 0.5342 (mm) REVERT: C 1294 LEU cc_start: 0.7806 (mt) cc_final: 0.7434 (mt) REVERT: C 1345 ILE cc_start: 0.5979 (mp) cc_final: 0.5342 (mt) REVERT: D 182 TYR cc_start: 0.7122 (t80) cc_final: 0.6230 (t80) REVERT: D 606 LEU cc_start: 0.6613 (mm) cc_final: 0.6391 (mm) REVERT: D 719 GLU cc_start: 0.6338 (tt0) cc_final: 0.5464 (mt-10) REVERT: D 757 SER cc_start: 0.8609 (p) cc_final: 0.8298 (p) REVERT: D 770 LEU cc_start: 0.6719 (pt) cc_final: 0.6079 (pp) REVERT: D 835 MET cc_start: 0.7973 (mmm) cc_final: 0.7653 (mmm) REVERT: D 989 ARG cc_start: 0.7573 (ptm160) cc_final: 0.7305 (ptm-80) REVERT: D 1097 PHE cc_start: 0.5975 (t80) cc_final: 0.5733 (t80) REVERT: D 1105 MET cc_start: 0.6079 (mtt) cc_final: 0.5867 (mtt) outliers start: 3 outliers final: 0 residues processed: 622 average time/residue: 0.1963 time to fit residues: 200.6901 Evaluate side-chains 501 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 225 optimal weight: 1.9990 chunk 300 optimal weight: 7.9990 chunk 177 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 218 optimal weight: 0.0050 chunk 395 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** A1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 708 GLN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 HIS ** C1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1371 ASN D 30 ASN D 355 ASN D 528 GLN D 708 GLN D 970 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.183773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.157101 restraints weight = 72973.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.156025 restraints weight = 82299.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.158039 restraints weight = 68229.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.157992 restraints weight = 44473.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.158351 restraints weight = 42014.425| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36050 Z= 0.125 Angle : 0.632 12.754 48828 Z= 0.321 Chirality : 0.045 0.255 5596 Planarity : 0.004 0.050 6294 Dihedral : 5.057 25.012 4816 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.55 % Favored : 91.42 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.12), residues: 4454 helix: -0.81 (0.16), residues: 1058 sheet: -1.24 (0.16), residues: 1032 loop : -2.52 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1335 TYR 0.016 0.001 TYR D1048 PHE 0.023 0.001 PHE C 347 TRP 0.036 0.002 TRP C 726 HIS 0.011 0.001 HIS D 789 Details of bonding type rmsd covalent geometry : bond 0.00286 (36046) covalent geometry : angle 0.63204 (48820) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.71718 ( 8) hydrogen bonds : bond 0.02894 ( 883) hydrogen bonds : angle 5.47634 ( 2352) =============================================================================== Job complete usr+sys time: 6120.77 seconds wall clock time: 106 minutes 30.05 seconds (6390.05 seconds total)