Starting phenix.real_space_refine on Sun Jun 29 17:48:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7b_31765/06_2025/7v7b_31765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7b_31765/06_2025/7v7b_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_31765/06_2025/7v7b_31765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7b_31765/06_2025/7v7b_31765.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7b_31765/06_2025/7v7b_31765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7b_31765/06_2025/7v7b_31765.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 42.42, per 1000 atoms: 1.20 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: 7.55 Conformation dependent library (CDL) restraints added in 4.3 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: 4.94 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: 15.86 Time building geometry restraints manager: 9.09 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: 0.17 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: 2.270 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: 1.280 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 99.690 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.440 ------------------------------------------------------------------------------- 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 : 5.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.028 0.003 TRP A 447 HIS 0.008 0.002 HIS B 240 PHE 0.023 0.002 PHE D 226 TYR 0.018 0.002 TYR A 808 ARG 0.008 0.001 ARG A1087 Details of bonding type rmsd hydrogen bonds : bond 0.30454 ( 883) hydrogen bonds : angle 10.94705 ( 2352) SS BOND : bond 0.01494 ( 4) SS BOND : angle 1.93521 ( 8) covalent geometry : bond 0.00443 (36046) covalent geometry : angle 0.91598 (48820) *********************** 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 : 4.433 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: A 9 ASP cc_start: 0.4683 (t0) cc_final: 0.4118 (m-30) REVERT: A 85 MET cc_start: 0.1327 (tpt) cc_final: -0.0120 (ttm) REVERT: A 179 LEU cc_start: 0.7697 (tp) cc_final: 0.7455 (tp) REVERT: A 753 GLN cc_start: 0.7729 (mt0) cc_final: 0.7447 (mt0) REVERT: A 773 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7138 (mm-40) REVERT: A 1166 MET cc_start: 0.1184 (mmm) cc_final: 0.0639 (ptm) REVERT: A 1288 LEU cc_start: 0.8270 (mp) cc_final: 0.8020 (tt) REVERT: A 1304 THR cc_start: 0.7588 (p) cc_final: 0.7177 (t) REVERT: B 155 PHE cc_start: 0.6051 (m-10) cc_final: 0.5813 (m-10) REVERT: B 166 ASP cc_start: 0.8585 (t0) cc_final: 0.8311 (t70) REVERT: B 182 TYR cc_start: 0.7132 (t80) cc_final: 0.6122 (t80) REVERT: B 246 LEU cc_start: 0.7909 (mp) cc_final: 0.7698 (mp) REVERT: B 284 LEU cc_start: 0.7072 (mp) cc_final: 0.6548 (mp) REVERT: B 355 ASN cc_start: 0.8508 (t0) cc_final: 0.8164 (t0) REVERT: B 693 LEU cc_start: 0.5534 (mp) cc_final: 0.4039 (mp) REVERT: B 723 LYS cc_start: 0.6938 (mttm) cc_final: 0.6298 (mmtp) REVERT: B 860 THR cc_start: 0.6317 (m) cc_final: 0.5829 (m) REVERT: B 973 ASN cc_start: 0.7783 (m-40) cc_final: 0.7497 (m-40) REVERT: B 1048 TYR cc_start: 0.7646 (t80) cc_final: 0.7419 (t80) REVERT: B 1114 TYR cc_start: 0.5545 (t80) cc_final: 0.5226 (t80) REVERT: C 9 ASP cc_start: 0.4792 (t0) cc_final: 0.4132 (m-30) REVERT: C 85 MET cc_start: 0.1263 (tpt) cc_final: -0.0168 (ttm) REVERT: C 179 LEU cc_start: 0.7748 (tp) cc_final: 0.7511 (tp) REVERT: C 753 GLN cc_start: 0.7736 (mt0) cc_final: 0.7401 (mt0) REVERT: C 773 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7035 (mm-40) REVERT: C 1084 SER cc_start: 0.7389 (p) cc_final: 0.7176 (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: 0.8054 (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: 0.8195 (tp30) REVERT: D 355 ASN cc_start: 0.8491 (t0) cc_final: 0.8116 (t0) REVERT: D 606 LEU cc_start: 0.6545 (mm) cc_final: 0.6317 (mt) REVERT: D 722 ARG cc_start: 0.5019 (mmm160) cc_final: 0.4700 (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: 0.7614 (m-40) REVERT: D 1097 PHE cc_start: 0.6553 (t80) cc_final: 0.6299 (t80) REVERT: D 1114 TYR cc_start: 0.5595 (t80) cc_final: 0.5310 (t80) outliers start: 0 outliers final: 0 residues processed: 1103 average time/residue: 0.5287 time to fit residues: 917.3329 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 : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 378 optimal weight: 9.9990 chunk 339 optimal weight: 0.0980 chunk 188 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 351 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 406 optimal weight: 7.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 394 HIS A 433 HIS A 497 ASN A 553 HIS A 687 ASN A 773 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1074 HIS A1174 HIS A1201 HIS A1253 HIS A1261 ASN A1289 HIS ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 163 HIS B 209 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 536 HIS ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 ASN B 796 GLN B 885 ASN B 905 HIS B 993 GLN B1005 ASN B1055 GLN C 394 HIS C 433 HIS C 497 ASN C 553 HIS C 687 ASN C 773 GLN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1015 GLN C1074 HIS C1174 HIS C1201 HIS C1253 HIS C1261 ASN C1289 HIS ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN D 163 HIS D 209 GLN ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 ASN D 796 GLN D 803 HIS D 885 ASN D 905 HIS D 993 GLN D1005 ASN D1055 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.182755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.155387 restraints weight = 71629.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.154628 restraints weight = 83435.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.156572 restraints weight = 69104.540| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 36050 Z= 0.195 Angle : 0.735 10.215 48828 Z= 0.385 Chirality : 0.047 0.151 5596 Planarity : 0.006 0.056 6294 Dihedral : 6.300 32.331 4816 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.11), residues: 4454 helix: -2.76 (0.13), residues: 1008 sheet: -2.12 (0.16), residues: 984 loop : -3.08 (0.11), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 447 HIS 0.008 0.002 HIS C 531 PHE 0.021 0.002 PHE A1301 TYR 0.030 0.002 TYR C1223 ARG 0.006 0.001 ARG D1102 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 883) hydrogen bonds : angle 7.32124 ( 2352) SS BOND : bond 0.00504 ( 4) SS BOND : angle 1.52492 ( 8) covalent geometry : bond 0.00438 (36046) covalent geometry : angle 0.73470 (48820) *********************** 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 755 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 752 time to evaluate : 3.983 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: A 9 ASP cc_start: 0.4148 (t0) cc_final: 0.3922 (m-30) REVERT: A 85 MET cc_start: 0.0770 (tpt) cc_final: -0.1085 (ttm) REVERT: A 515 GLN cc_start: 0.7276 (tt0) cc_final: 0.7063 (mm110) REVERT: A 571 MET cc_start: 0.8238 (mmm) cc_final: 0.8026 (mmt) REVERT: A 616 ARG cc_start: 0.6922 (ptt-90) cc_final: 0.5755 (ptm-80) REVERT: A 773 GLN cc_start: 0.7716 (tm130) cc_final: 0.7179 (mp10) REVERT: A 1166 MET cc_start: 0.0688 (mmm) cc_final: -0.0177 (ptm) REVERT: A 1186 LYS cc_start: 0.5521 (mmmt) cc_final: 0.4916 (mmmm) REVERT: A 1288 LEU cc_start: 0.8251 (mp) cc_final: 0.7943 (tt) REVERT: A 1304 THR cc_start: 0.7537 (p) cc_final: 0.7163 (t) REVERT: B 182 TYR cc_start: 0.6952 (t80) cc_final: 0.6086 (t80) REVERT: B 355 ASN cc_start: 0.8528 (t0) cc_final: 0.8302 (t0) REVERT: B 679 MET cc_start: 0.5068 (mmm) cc_final: 0.4424 (tmm) REVERT: B 723 LYS cc_start: 0.7059 (mttm) cc_final: 0.6369 (mmtp) REVERT: B 973 ASN cc_start: 0.8086 (m-40) cc_final: 0.7471 (m-40) REVERT: B 1114 TYR cc_start: 0.5792 (t80) cc_final: 0.4976 (t80) REVERT: C 9 ASP cc_start: 0.4103 (t0) cc_final: 0.3847 (m-30) REVERT: C 85 MET cc_start: 0.0826 (tpt) cc_final: -0.0892 (ttm) REVERT: C 515 GLN cc_start: 0.7263 (tt0) cc_final: 0.7031 (mm110) REVERT: C 616 ARG cc_start: 0.6900 (ptt-90) cc_final: 0.5745 (ptm-80) REVERT: C 773 GLN cc_start: 0.7668 (tm130) cc_final: 0.7151 (mp10) REVERT: C 814 GLU cc_start: 0.8147 (tp30) cc_final: 0.7899 (tp30) REVERT: C 1166 MET cc_start: 0.0713 (mmm) cc_final: -0.0175 (ptm) REVERT: C 1186 LYS cc_start: 0.5508 (mmmt) cc_final: 0.4877 (mmmm) REVERT: C 1223 TYR cc_start: 0.7549 (m-80) cc_final: 0.7314 (t80) REVERT: C 1288 LEU cc_start: 0.8225 (mp) cc_final: 0.7967 (tt) REVERT: C 1304 THR cc_start: 0.7488 (p) cc_final: 0.7139 (t) REVERT: D 141 LYS cc_start: 0.7803 (mttt) cc_final: 0.7467 (mttm) REVERT: D 182 TYR cc_start: 0.7064 (t80) cc_final: 0.6024 (t80) REVERT: D 213 GLU cc_start: 0.8214 (tt0) cc_final: 0.7927 (tt0) REVERT: D 236 SER cc_start: 0.9062 (p) cc_final: 0.8541 (p) REVERT: D 355 ASN cc_start: 0.8607 (t0) cc_final: 0.8379 (t0) REVERT: D 606 LEU cc_start: 0.6387 (mm) cc_final: 0.6123 (mt) REVERT: D 679 MET cc_start: 0.5273 (mmm) cc_final: 0.4351 (tmm) REVERT: D 916 THR cc_start: 0.7962 (p) cc_final: 0.7603 (t) REVERT: D 973 ASN cc_start: 0.8065 (m-40) cc_final: 0.7431 (m-40) REVERT: D 1114 TYR cc_start: 0.6064 (t80) cc_final: 0.5712 (t80) outliers start: 3 outliers final: 2 residues processed: 755 average time/residue: 0.5103 time to fit residues: 618.7007 Evaluate side-chains 520 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 518 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 147 optimal weight: 8.9990 chunk 341 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 338 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 370 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 387 optimal weight: 30.0000 chunk 331 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 437 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 519 HIS A 720 HIS A 788 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B 759 GLN C 102 ASN C 183 GLN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 720 HIS C 788 GLN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 HIS ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 GLN ** D 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN D 759 GLN D1034 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.181250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.153159 restraints weight = 71518.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.151778 restraints weight = 91333.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.153714 restraints weight = 75921.208| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36050 Z= 0.179 Angle : 0.691 8.776 48828 Z= 0.360 Chirality : 0.046 0.266 5596 Planarity : 0.005 0.053 6294 Dihedral : 6.094 30.050 4816 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.11), residues: 4454 helix: -2.18 (0.14), residues: 1068 sheet: -2.00 (0.16), residues: 1020 loop : -3.04 (0.11), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 447 HIS 0.007 0.001 HIS B 240 PHE 0.019 0.002 PHE A1077 TYR 0.023 0.002 TYR A1223 ARG 0.006 0.001 ARG C 772 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 883) hydrogen bonds : angle 6.71114 ( 2352) SS BOND : bond 0.00523 ( 4) SS BOND : angle 1.44128 ( 8) covalent geometry : bond 0.00404 (36046) covalent geometry : angle 0.69070 (48820) *********************** 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 666 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 4.050 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: A 9 ASP cc_start: 0.4081 (t0) cc_final: 0.3870 (m-30) REVERT: A 85 MET cc_start: 0.1124 (tpt) cc_final: -0.0890 (ttm) REVERT: A 432 MET cc_start: 0.5949 (pmm) cc_final: 0.5723 (pmm) REVERT: A 773 GLN cc_start: 0.7585 (pp30) cc_final: 0.7172 (mp10) REVERT: A 814 GLU cc_start: 0.8354 (tp30) cc_final: 0.8115 (tp30) REVERT: A 1166 MET cc_start: 0.0874 (mmm) cc_final: -0.0127 (ptm) REVERT: A 1186 LYS cc_start: 0.5845 (mmmt) cc_final: 0.5421 (mmmm) REVERT: A 1304 THR cc_start: 0.7611 (p) cc_final: 0.7309 (t) REVERT: B 182 TYR cc_start: 0.6818 (t80) cc_final: 0.6005 (t80) REVERT: B 355 ASN cc_start: 0.8673 (t0) cc_final: 0.8178 (t0) REVERT: B 449 MET cc_start: 0.1259 (mmm) cc_final: 0.0827 (mmp) REVERT: B 679 MET cc_start: 0.4276 (mmm) cc_final: 0.3996 (ppp) REVERT: B 1104 LYS cc_start: 0.7771 (mmpt) cc_final: 0.7374 (tppt) REVERT: C 9 ASP cc_start: 0.4061 (t0) cc_final: 0.3851 (m-30) REVERT: C 85 MET cc_start: 0.1052 (tpt) cc_final: -0.0940 (ttm) REVERT: C 325 ILE cc_start: 0.7528 (mt) cc_final: 0.7328 (mt) REVERT: C 773 GLN cc_start: 0.7585 (pp30) cc_final: 0.7124 (mp10) REVERT: C 845 PHE cc_start: 0.3995 (p90) cc_final: 0.3680 (p90) REVERT: C 1166 MET cc_start: 0.0680 (mmm) cc_final: -0.0294 (ptm) REVERT: C 1186 LYS cc_start: 0.5792 (mmmt) cc_final: 0.5371 (mmmm) REVERT: C 1304 THR cc_start: 0.7561 (p) cc_final: 0.7254 (t) REVERT: D 64 MET cc_start: 0.8430 (pmm) cc_final: 0.7943 (pmm) REVERT: D 182 TYR cc_start: 0.7040 (t80) cc_final: 0.6077 (t80) REVERT: D 213 GLU cc_start: 0.8217 (tt0) cc_final: 0.7862 (tt0) REVERT: D 236 SER cc_start: 0.9027 (p) cc_final: 0.8381 (p) REVERT: D 355 ASN cc_start: 0.8740 (t0) cc_final: 0.8281 (t0) REVERT: D 449 MET cc_start: 0.1026 (mmm) cc_final: 0.0815 (mmp) REVERT: D 606 LEU cc_start: 0.6382 (mm) cc_final: 0.6180 (mm) REVERT: D 679 MET cc_start: 0.5535 (mmm) cc_final: 0.4648 (tmm) REVERT: D 973 ASN cc_start: 0.8006 (m-40) cc_final: 0.7368 (m-40) REVERT: D 1104 LYS cc_start: 0.7714 (mmpt) cc_final: 0.7374 (tppt) REVERT: D 1105 MET cc_start: 0.7254 (mtp) cc_final: 0.6780 (mtt) REVERT: D 1114 TYR cc_start: 0.6219 (t80) cc_final: 0.5980 (t80) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.4834 time to fit residues: 524.4984 Evaluate side-chains 494 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 4.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 410 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 435 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 418 optimal weight: 0.4980 chunk 128 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** 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 343 GLN B 531 HIS B 672 ASN B 708 GLN B 759 GLN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS D 536 HIS D 708 GLN D 759 GLN D 803 HIS D1034 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.180780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.153646 restraints weight = 71551.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.152366 restraints weight = 97970.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.154147 restraints weight = 82467.924| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36050 Z= 0.160 Angle : 0.651 7.733 48828 Z= 0.338 Chirality : 0.046 0.152 5596 Planarity : 0.005 0.050 6294 Dihedral : 5.867 27.208 4816 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.11), residues: 4454 helix: -1.84 (0.15), residues: 1058 sheet: -1.86 (0.16), residues: 996 loop : -2.90 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 953 HIS 0.005 0.001 HIS D 240 PHE 0.017 0.002 PHE A1301 TYR 0.022 0.002 TYR D1048 ARG 0.012 0.000 ARG B 655 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 883) hydrogen bonds : angle 6.29503 ( 2352) SS BOND : bond 0.00414 ( 4) SS BOND : angle 1.26100 ( 8) covalent geometry : bond 0.00364 (36046) covalent geometry : angle 0.65048 (48820) *********************** 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 634 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 3.891 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 9 ASP cc_start: 0.4061 (t0) cc_final: 0.3844 (m-30) REVERT: A 85 MET cc_start: 0.1904 (tpt) cc_final: -0.0036 (ttm) REVERT: A 399 LYS cc_start: 0.7118 (tptp) cc_final: 0.6827 (tptt) REVERT: A 773 GLN cc_start: 0.7690 (pp30) cc_final: 0.7144 (mp10) REVERT: A 814 GLU cc_start: 0.8171 (tp30) cc_final: 0.7665 (tp30) REVERT: A 845 PHE cc_start: 0.4231 (p90) cc_final: 0.3813 (p90) REVERT: A 1166 MET cc_start: 0.0741 (mmm) cc_final: -0.0299 (ptm) REVERT: B 182 TYR cc_start: 0.6844 (t80) cc_final: 0.5889 (t80) REVERT: B 215 GLU cc_start: 0.6381 (mm-30) cc_final: 0.6058 (mp0) REVERT: B 355 ASN cc_start: 0.8761 (t0) cc_final: 0.8282 (t0) REVERT: B 449 MET cc_start: 0.1774 (mmm) cc_final: 0.0476 (mmt) REVERT: B 722 ARG cc_start: 0.6073 (mmp-170) cc_final: 0.5813 (mmp-170) REVERT: B 1014 MET cc_start: 0.5166 (mmt) cc_final: 0.4935 (mmm) REVERT: B 1092 ASP cc_start: 0.7975 (m-30) cc_final: 0.7713 (m-30) REVERT: B 1104 LYS cc_start: 0.7701 (mmpt) cc_final: 0.7412 (tppt) REVERT: C 9 ASP cc_start: 0.4037 (t0) cc_final: 0.3822 (m-30) REVERT: C 85 MET cc_start: 0.1866 (tpt) cc_final: -0.0053 (ttm) REVERT: C 616 ARG cc_start: 0.6788 (ptt-90) cc_final: 0.6494 (ptp90) REVERT: C 773 GLN cc_start: 0.7698 (pp30) cc_final: 0.7146 (mp10) REVERT: C 845 PHE cc_start: 0.4094 (p90) cc_final: 0.3651 (p90) REVERT: C 1166 MET cc_start: 0.0712 (mmm) cc_final: -0.0320 (ptm) REVERT: C 1304 THR cc_start: 0.7519 (p) cc_final: 0.7266 (t) REVERT: D 182 TYR cc_start: 0.6979 (t80) cc_final: 0.6029 (t80) REVERT: D 213 GLU cc_start: 0.8215 (tt0) cc_final: 0.7792 (tt0) REVERT: D 236 SER cc_start: 0.9083 (p) cc_final: 0.8524 (p) REVERT: D 355 ASN cc_start: 0.8761 (t0) cc_final: 0.8365 (t0) REVERT: D 679 MET cc_start: 0.5305 (mmm) cc_final: 0.4563 (tmm) REVERT: D 973 ASN cc_start: 0.8264 (m-40) cc_final: 0.8050 (m-40) REVERT: D 989 ARG cc_start: 0.7638 (ptm160) cc_final: 0.7166 (ptm-80) REVERT: D 1014 MET cc_start: 0.3883 (tpt) cc_final: 0.3351 (tpt) REVERT: D 1092 ASP cc_start: 0.8150 (m-30) cc_final: 0.7599 (m-30) REVERT: D 1104 LYS cc_start: 0.7707 (mmpt) cc_final: 0.7412 (tppt) outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.4721 time to fit residues: 487.3693 Evaluate side-chains 485 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 370 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 427 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 416 optimal weight: 7.9990 chunk 283 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B 759 GLN ** B1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 520 GLN D 708 GLN D 759 GLN ** D 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.177853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.148870 restraints weight = 70979.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.147559 restraints weight = 94241.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.149063 restraints weight = 73631.838| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 36050 Z= 0.197 Angle : 0.703 8.144 48828 Z= 0.364 Chirality : 0.047 0.146 5596 Planarity : 0.005 0.048 6294 Dihedral : 6.013 27.478 4816 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.00 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.11), residues: 4454 helix: -1.85 (0.14), residues: 1044 sheet: -1.96 (0.16), residues: 1014 loop : -2.86 (0.11), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 610 HIS 0.008 0.001 HIS A 802 PHE 0.032 0.002 PHE D1088 TYR 0.029 0.002 TYR C1223 ARG 0.012 0.001 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 883) hydrogen bonds : angle 6.37510 ( 2352) SS BOND : bond 0.00588 ( 4) SS BOND : angle 1.34650 ( 8) covalent geometry : bond 0.00451 (36046) covalent geometry : angle 0.70306 (48820) *********************** 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 598 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 598 time to evaluate : 5.556 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: A 85 MET cc_start: 0.1581 (tpt) cc_final: -0.0315 (ttm) REVERT: A 399 LYS cc_start: 0.7260 (tptp) cc_final: 0.6885 (tptt) REVERT: A 814 GLU cc_start: 0.8152 (tp30) cc_final: 0.7612 (tp30) REVERT: A 845 PHE cc_start: 0.4222 (p90) cc_final: 0.3585 (p90) REVERT: A 1166 MET cc_start: 0.1074 (mmm) cc_final: -0.0202 (ptm) REVERT: A 1304 THR cc_start: 0.7501 (p) cc_final: 0.7247 (t) REVERT: B 182 TYR cc_start: 0.6806 (t80) cc_final: 0.5938 (t80) REVERT: B 355 ASN cc_start: 0.8862 (t0) cc_final: 0.8079 (t0) REVERT: B 449 MET cc_start: 0.1984 (mmm) cc_final: 0.0683 (mmt) REVERT: B 679 MET cc_start: 0.3748 (ppp) cc_final: 0.3493 (ppp) REVERT: B 722 ARG cc_start: 0.6395 (mmp-170) cc_final: 0.5895 (mmp-170) REVERT: B 989 ARG cc_start: 0.7897 (ptm160) cc_final: 0.6956 (ttp-170) REVERT: B 1014 MET cc_start: 0.5326 (mmt) cc_final: 0.5043 (mmm) REVERT: B 1104 LYS cc_start: 0.7691 (mmpt) cc_final: 0.7445 (tppt) REVERT: C 85 MET cc_start: 0.1570 (tpt) cc_final: -0.0345 (ttm) REVERT: C 572 MET cc_start: 0.7610 (ptp) cc_final: 0.7366 (ptm) REVERT: C 773 GLN cc_start: 0.7834 (pp30) cc_final: 0.6971 (mp10) REVERT: C 845 PHE cc_start: 0.4087 (p90) cc_final: 0.3481 (p90) REVERT: C 1166 MET cc_start: 0.1022 (mmm) cc_final: -0.0238 (ptm) REVERT: D 182 TYR cc_start: 0.6970 (t80) cc_final: 0.6006 (t80) REVERT: D 355 ASN cc_start: 0.8847 (t0) cc_final: 0.7946 (t0) REVERT: D 606 LEU cc_start: 0.6715 (mm) cc_final: 0.6484 (mm) REVERT: D 679 MET cc_start: 0.5414 (mmm) cc_final: 0.4369 (tmm) REVERT: D 989 ARG cc_start: 0.7818 (ptm160) cc_final: 0.7391 (ptm-80) REVERT: D 1104 LYS cc_start: 0.7649 (mmpt) cc_final: 0.7440 (tppt) outliers start: 0 outliers final: 0 residues processed: 598 average time/residue: 0.4710 time to fit residues: 466.5522 Evaluate side-chains 471 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 4.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 139 optimal weight: 0.9980 chunk 434 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 283 optimal weight: 0.5980 chunk 302 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.0040 chunk 158 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 788 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 HIS ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 708 GLN B 789 HIS C 788 GLN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1187 HIS ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN D 789 HIS D 803 HIS D 970 ASN D1077 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.184222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.156350 restraints weight = 70073.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.154449 restraints weight = 88737.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.156294 restraints weight = 70781.692| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 36050 Z= 0.108 Angle : 0.608 8.389 48828 Z= 0.311 Chirality : 0.045 0.368 5596 Planarity : 0.004 0.048 6294 Dihedral : 5.436 25.423 4816 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.12), residues: 4454 helix: -1.39 (0.15), residues: 1038 sheet: -1.64 (0.16), residues: 1034 loop : -2.71 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 610 HIS 0.004 0.001 HIS A1187 PHE 0.017 0.001 PHE C 470 TYR 0.026 0.001 TYR D1048 ARG 0.007 0.000 ARG C 772 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 883) hydrogen bonds : angle 5.72473 ( 2352) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.82868 ( 8) covalent geometry : bond 0.00240 (36046) covalent geometry : angle 0.60812 (48820) *********************** 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 664 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 664 time to evaluate : 3.979 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 9 ASP cc_start: 0.3951 (t0) cc_final: 0.3690 (m-30) REVERT: A 85 MET cc_start: 0.1363 (tpt) cc_final: -0.0392 (ttm) REVERT: A 348 MET cc_start: 0.6323 (mtp) cc_final: 0.6064 (mmm) REVERT: A 402 GLU cc_start: 0.6711 (mt-10) cc_final: 0.5648 (tp30) REVERT: A 432 MET cc_start: 0.5588 (pmm) cc_final: 0.5346 (pmm) REVERT: A 572 MET cc_start: 0.7452 (ptp) cc_final: 0.7051 (ptp) REVERT: A 726 TRP cc_start: 0.7402 (m-10) cc_final: 0.6704 (m-10) REVERT: A 753 GLN cc_start: 0.7196 (tt0) cc_final: 0.6284 (tp-100) REVERT: A 773 GLN cc_start: 0.7613 (pp30) cc_final: 0.6976 (mp10) REVERT: A 814 GLU cc_start: 0.8082 (tp30) cc_final: 0.7566 (tp30) REVERT: A 845 PHE cc_start: 0.4022 (p90) cc_final: 0.3503 (p90) REVERT: A 1166 MET cc_start: 0.0955 (mmm) cc_final: -0.0147 (ptm) REVERT: A 1304 THR cc_start: 0.7272 (p) cc_final: 0.7037 (t) REVERT: A 1345 ILE cc_start: 0.5980 (mp) cc_final: 0.5262 (mt) REVERT: B 64 MET cc_start: 0.8324 (pmm) cc_final: 0.7773 (pmm) REVERT: B 133 LEU cc_start: 0.7550 (mt) cc_final: 0.7350 (mt) REVERT: B 135 LEU cc_start: 0.7616 (mt) cc_final: 0.7410 (mt) REVERT: B 182 TYR cc_start: 0.6734 (t80) cc_final: 0.5794 (t80) REVERT: B 449 MET cc_start: 0.1767 (mmm) cc_final: 0.0527 (mmt) REVERT: B 722 ARG cc_start: 0.6415 (mmp-170) cc_final: 0.5928 (mmp-170) REVERT: B 989 ARG cc_start: 0.7659 (ptm160) cc_final: 0.6542 (ttp-170) REVERT: B 1014 MET cc_start: 0.5096 (mmt) cc_final: 0.4825 (mmm) REVERT: B 1065 VAL cc_start: 0.5074 (t) cc_final: 0.4400 (t) REVERT: B 1104 LYS cc_start: 0.7685 (mmpt) cc_final: 0.7473 (tppt) REVERT: C 9 ASP cc_start: 0.3878 (t0) cc_final: 0.3659 (m-30) REVERT: C 85 MET cc_start: 0.1365 (tpt) cc_final: -0.0409 (ttm) REVERT: C 357 MET cc_start: 0.5790 (mmm) cc_final: 0.5574 (mmm) REVERT: C 399 LYS cc_start: 0.6907 (tptp) cc_final: 0.6702 (tptt) REVERT: C 572 MET cc_start: 0.7484 (ptp) cc_final: 0.7110 (ptp) REVERT: C 726 TRP cc_start: 0.7377 (m-10) cc_final: 0.6730 (m-10) REVERT: C 753 GLN cc_start: 0.7293 (tt0) cc_final: 0.6304 (tp-100) REVERT: C 773 GLN cc_start: 0.7585 (pp30) cc_final: 0.6913 (mp10) REVERT: C 845 PHE cc_start: 0.3856 (p90) cc_final: 0.3319 (p90) REVERT: C 1166 MET cc_start: 0.0918 (mmm) cc_final: -0.0166 (ptm) REVERT: C 1304 THR cc_start: 0.7333 (p) cc_final: 0.7115 (t) REVERT: C 1345 ILE cc_start: 0.5820 (mp) cc_final: 0.5131 (mt) REVERT: D 133 LEU cc_start: 0.7494 (mt) cc_final: 0.7230 (mt) REVERT: D 182 TYR cc_start: 0.6934 (t80) cc_final: 0.5959 (t80) REVERT: D 192 THR cc_start: 0.7583 (p) cc_final: 0.7380 (p) REVERT: D 679 MET cc_start: 0.5062 (mmm) cc_final: 0.4358 (tmm) REVERT: D 892 GLU cc_start: 0.5875 (tt0) cc_final: 0.5423 (tt0) REVERT: D 989 ARG cc_start: 0.7619 (ptm160) cc_final: 0.7131 (ptm-80) REVERT: D 1104 LYS cc_start: 0.7808 (mmpt) cc_final: 0.7530 (tppt) outliers start: 0 outliers final: 0 residues processed: 664 average time/residue: 0.4623 time to fit residues: 503.9344 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 : 3.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 442 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 HIS ** A1189 GLN ** 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 C 183 GLN C 519 HIS ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1187 HIS ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN D 759 GLN D 789 HIS D 803 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.182084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.154331 restraints weight = 71658.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.152938 restraints weight = 92414.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.154978 restraints weight = 76135.717| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36050 Z= 0.128 Angle : 0.625 8.028 48828 Z= 0.319 Chirality : 0.045 0.235 5596 Planarity : 0.004 0.047 6294 Dihedral : 5.350 25.426 4816 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.43 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.12), residues: 4454 helix: -1.34 (0.15), residues: 1072 sheet: -1.54 (0.16), residues: 1008 loop : -2.70 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 610 HIS 0.007 0.001 HIS B 789 PHE 0.017 0.002 PHE C1355 TYR 0.023 0.001 TYR D 812 ARG 0.005 0.000 ARG C 772 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 883) hydrogen bonds : angle 5.70520 ( 2352) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.86558 ( 8) covalent geometry : bond 0.00290 (36046) covalent geometry : angle 0.62505 (48820) *********************** 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 622 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 3.839 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: A 9 ASP cc_start: 0.3861 (t0) cc_final: 0.3661 (m-30) REVERT: A 85 MET cc_start: 0.1274 (tpt) cc_final: -0.0471 (ttm) REVERT: A 348 MET cc_start: 0.6395 (mtp) cc_final: 0.5942 (mmm) REVERT: A 427 MET cc_start: 0.5281 (tpt) cc_final: 0.5002 (tpp) REVERT: A 572 MET cc_start: 0.7607 (ptp) cc_final: 0.7232 (ptp) REVERT: A 612 THR cc_start: 0.7531 (m) cc_final: 0.7265 (m) REVERT: A 726 TRP cc_start: 0.7353 (m-10) cc_final: 0.6356 (m-10) REVERT: A 753 GLN cc_start: 0.7327 (tt0) cc_final: 0.6550 (tp-100) REVERT: A 773 GLN cc_start: 0.7598 (pp30) cc_final: 0.6989 (mp10) REVERT: A 814 GLU cc_start: 0.8151 (tp30) cc_final: 0.7656 (tp30) REVERT: A 845 PHE cc_start: 0.4058 (p90) cc_final: 0.3464 (p90) REVERT: A 1166 MET cc_start: 0.1135 (mmm) cc_final: -0.0203 (ptm) REVERT: A 1172 MET cc_start: 0.6661 (tpp) cc_final: 0.6433 (tpt) REVERT: A 1259 ASN cc_start: 0.7134 (t0) cc_final: 0.6852 (t0) REVERT: A 1304 THR cc_start: 0.7356 (p) cc_final: 0.7121 (t) REVERT: B 182 TYR cc_start: 0.6752 (t80) cc_final: 0.5814 (t80) REVERT: B 449 MET cc_start: 0.1890 (mmm) cc_final: 0.0642 (mmt) REVERT: B 835 MET cc_start: 0.7737 (mmp) cc_final: 0.7285 (mmm) REVERT: B 989 ARG cc_start: 0.7819 (ptm160) cc_final: 0.6740 (ttp-170) REVERT: B 1014 MET cc_start: 0.5191 (mmt) cc_final: 0.4862 (mmm) REVERT: B 1104 LYS cc_start: 0.7682 (mmpt) cc_final: 0.7399 (tppt) REVERT: B 1105 MET cc_start: 0.6012 (mtt) cc_final: 0.5551 (mtt) REVERT: C 85 MET cc_start: 0.1340 (tpt) cc_final: -0.0472 (ttm) REVERT: C 357 MET cc_start: 0.5807 (mmm) cc_final: 0.5597 (mmm) REVERT: C 399 LYS cc_start: 0.6961 (tptp) cc_final: 0.6572 (tptt) REVERT: C 572 MET cc_start: 0.7703 (ptp) cc_final: 0.7355 (ptp) REVERT: C 726 TRP cc_start: 0.7401 (m-10) cc_final: 0.7003 (m-10) REVERT: C 753 GLN cc_start: 0.7383 (tt0) cc_final: 0.6581 (tp-100) REVERT: C 773 GLN cc_start: 0.7759 (pp30) cc_final: 0.6909 (mp10) REVERT: C 845 PHE cc_start: 0.3911 (p90) cc_final: 0.3250 (p90) REVERT: C 1166 MET cc_start: 0.1107 (mmm) cc_final: -0.0245 (ptm) REVERT: C 1223 TYR cc_start: 0.7504 (m-10) cc_final: 0.7252 (m-10) REVERT: C 1304 THR cc_start: 0.7309 (p) cc_final: 0.7080 (t) REVERT: D 182 TYR cc_start: 0.6855 (t80) cc_final: 0.5935 (t80) REVERT: D 606 LEU cc_start: 0.6524 (mm) cc_final: 0.6308 (mm) REVERT: D 679 MET cc_start: 0.5021 (mmm) cc_final: 0.4322 (ppp) REVERT: D 989 ARG cc_start: 0.7701 (ptm160) cc_final: 0.7278 (ptm-80) REVERT: D 1104 LYS cc_start: 0.7734 (mmpt) cc_final: 0.7455 (tppt) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.4698 time to fit residues: 479.5017 Evaluate side-chains 489 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 404 optimal weight: 6.9990 chunk 432 optimal weight: 0.9980 chunk 341 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 447 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 231 optimal weight: 0.3980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 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 C 519 HIS ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1187 HIS ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 470 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN ** D1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1077 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.182798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.154871 restraints weight = 71220.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.153591 restraints weight = 99520.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.155647 restraints weight = 75953.474| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36050 Z= 0.117 Angle : 0.616 8.393 48828 Z= 0.312 Chirality : 0.045 0.241 5596 Planarity : 0.004 0.049 6294 Dihedral : 5.213 25.420 4816 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.76 % Favored : 91.22 % Rotamer: Outliers : 0.03 % Allowed : 0.86 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.12), residues: 4454 helix: -1.17 (0.15), residues: 1070 sheet: -1.56 (0.16), residues: 1034 loop : -2.64 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 610 HIS 0.016 0.001 HIS B 789 PHE 0.026 0.001 PHE B1097 TYR 0.015 0.001 TYR D 812 ARG 0.005 0.000 ARG A1335 Details of bonding type rmsd hydrogen bonds : bond 0.02898 ( 883) hydrogen bonds : angle 5.53036 ( 2352) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.81474 ( 8) covalent geometry : bond 0.00268 (36046) covalent geometry : angle 0.61579 (48820) *********************** 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 622 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 621 time to evaluate : 4.315 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: A 85 MET cc_start: 0.1286 (tpt) cc_final: -0.0366 (ttm) REVERT: A 348 MET cc_start: 0.6382 (mtp) cc_final: 0.6035 (mmm) REVERT: A 572 MET cc_start: 0.7703 (ptp) cc_final: 0.7332 (ptp) REVERT: A 726 TRP cc_start: 0.7160 (m-10) cc_final: 0.6051 (m-10) REVERT: A 753 GLN cc_start: 0.7399 (tt0) cc_final: 0.6543 (tp-100) REVERT: A 773 GLN cc_start: 0.7543 (pp30) cc_final: 0.6811 (mp10) REVERT: A 791 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7672 (mmmt) REVERT: A 845 PHE cc_start: 0.4049 (p90) cc_final: 0.3508 (p90) REVERT: A 1166 MET cc_start: 0.1237 (mmm) cc_final: -0.0173 (ptm) REVERT: A 1345 ILE cc_start: 0.5891 (mp) cc_final: 0.5114 (mt) REVERT: B 182 TYR cc_start: 0.6695 (t80) cc_final: 0.5772 (t80) REVERT: B 449 MET cc_start: 0.1775 (mmm) cc_final: 0.0692 (mmt) REVERT: B 989 ARG cc_start: 0.7797 (ptm160) cc_final: 0.6710 (ttp-170) REVERT: B 1014 MET cc_start: 0.5122 (mmt) cc_final: 0.4835 (mmm) REVERT: B 1097 PHE cc_start: 0.6354 (t80) cc_final: 0.6004 (t80) REVERT: B 1105 MET cc_start: 0.5997 (mtt) cc_final: 0.5521 (mtt) REVERT: C 85 MET cc_start: 0.1295 (tpt) cc_final: -0.0386 (ttm) REVERT: C 357 MET cc_start: 0.5814 (mmm) cc_final: 0.5564 (mmm) REVERT: C 399 LYS cc_start: 0.6970 (tptp) cc_final: 0.6486 (tptt) REVERT: C 572 MET cc_start: 0.7753 (ptp) cc_final: 0.7379 (ptp) REVERT: C 726 TRP cc_start: 0.7307 (m-10) cc_final: 0.6894 (m-10) REVERT: C 753 GLN cc_start: 0.7428 (tt0) cc_final: 0.6566 (tp-100) REVERT: C 773 GLN cc_start: 0.7728 (pp30) cc_final: 0.6892 (mp10) REVERT: C 845 PHE cc_start: 0.3820 (p90) cc_final: 0.3287 (p90) REVERT: C 1166 MET cc_start: 0.1226 (mmm) cc_final: -0.0229 (ptm) REVERT: C 1223 TYR cc_start: 0.7603 (m-10) cc_final: 0.7386 (m-10) REVERT: C 1345 ILE cc_start: 0.5965 (mp) cc_final: 0.5234 (mt) REVERT: D 130 MET cc_start: 0.6653 (ptt) cc_final: 0.6450 (ptp) REVERT: D 182 TYR cc_start: 0.6814 (t80) cc_final: 0.5952 (t80) REVERT: D 291 MET cc_start: 0.4660 (ttp) cc_final: 0.4352 (ptm) REVERT: D 679 MET cc_start: 0.5054 (mmm) cc_final: 0.4513 (ppp) REVERT: D 719 GLU cc_start: 0.6330 (tt0) cc_final: 0.5490 (mt-10) REVERT: D 757 SER cc_start: 0.8596 (p) cc_final: 0.8332 (p) REVERT: D 989 ARG cc_start: 0.7702 (ptm160) cc_final: 0.7251 (ptm-80) REVERT: D 1105 MET cc_start: 0.5951 (mtt) cc_final: 0.5541 (mtt) outliers start: 1 outliers final: 0 residues processed: 621 average time/residue: 0.4621 time to fit residues: 468.7823 Evaluate side-chains 467 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 208 optimal weight: 0.8980 chunk 404 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 209 optimal weight: 0.0020 chunk 354 optimal weight: 3.9990 chunk 359 optimal weight: 3.9990 chunk 393 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 379 optimal weight: 2.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 528 GLN B 708 GLN B 810 ASN ** B1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 519 HIS ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1371 ASN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 470 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 528 GLN D 708 GLN ** D1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.180492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.153157 restraints weight = 71785.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.151712 restraints weight = 94486.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.153096 restraints weight = 77639.516| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36050 Z= 0.145 Angle : 0.648 12.851 48828 Z= 0.331 Chirality : 0.046 0.256 5596 Planarity : 0.004 0.047 6294 Dihedral : 5.342 24.756 4816 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.24 % Favored : 89.74 % Rotamer: Outliers : 0.03 % Allowed : 0.81 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.12), residues: 4454 helix: -1.17 (0.15), residues: 1064 sheet: -1.42 (0.16), residues: 976 loop : -2.73 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 610 HIS 0.014 0.001 HIS D 789 PHE 0.025 0.002 PHE D1097 TYR 0.015 0.001 TYR D 812 ARG 0.005 0.000 ARG C 815 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 883) hydrogen bonds : angle 5.65790 ( 2352) SS BOND : bond 0.00318 ( 4) SS BOND : angle 0.90294 ( 8) covalent geometry : bond 0.00333 (36046) covalent geometry : angle 0.64826 (48820) *********************** 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 603 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 602 time to evaluate : 3.738 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: A 85 MET cc_start: 0.1249 (tpt) cc_final: -0.0498 (ttm) REVERT: A 348 MET cc_start: 0.6557 (mtp) cc_final: 0.6165 (mmm) REVERT: A 572 MET cc_start: 0.7828 (ptp) cc_final: 0.7487 (ptp) REVERT: A 753 GLN cc_start: 0.7434 (tt0) cc_final: 0.6634 (tp-100) REVERT: A 772 ARG cc_start: 0.7077 (mtm-85) cc_final: 0.6708 (ttm110) REVERT: A 773 GLN cc_start: 0.7647 (pp30) cc_final: 0.6791 (mp10) REVERT: A 791 LYS cc_start: 0.7977 (mmtm) cc_final: 0.7714 (mmmt) REVERT: A 845 PHE cc_start: 0.4205 (p90) cc_final: 0.3539 (p90) REVERT: A 1166 MET cc_start: 0.1725 (mmm) cc_final: -0.0098 (ptm) REVERT: B 182 TYR cc_start: 0.6725 (t80) cc_final: 0.5710 (t80) REVERT: B 449 MET cc_start: 0.1801 (mmm) cc_final: 0.0413 (mmt) REVERT: B 925 ASP cc_start: 0.7630 (t0) cc_final: 0.6995 (p0) REVERT: B 989 ARG cc_start: 0.7889 (ptm160) cc_final: 0.6845 (ttp-170) REVERT: B 1014 MET cc_start: 0.5204 (mmt) cc_final: 0.4918 (mmm) REVERT: B 1097 PHE cc_start: 0.6444 (t80) cc_final: 0.6215 (t80) REVERT: B 1105 MET cc_start: 0.6016 (mtt) cc_final: 0.5432 (mtt) REVERT: C 85 MET cc_start: 0.1348 (tpt) cc_final: -0.0389 (ttm) REVERT: C 357 MET cc_start: 0.5783 (mmm) cc_final: 0.5495 (mmm) REVERT: C 399 LYS cc_start: 0.7008 (tptp) cc_final: 0.6751 (tptt) REVERT: C 572 MET cc_start: 0.7815 (ptp) cc_final: 0.7469 (ptp) REVERT: C 726 TRP cc_start: 0.7440 (m-10) cc_final: 0.6903 (m-10) REVERT: C 753 GLN cc_start: 0.7517 (tt0) cc_final: 0.6598 (tp-100) REVERT: C 1166 MET cc_start: 0.1663 (mmm) cc_final: -0.0103 (ptm) REVERT: C 1223 TYR cc_start: 0.7752 (m-10) cc_final: 0.7484 (m-10) REVERT: D 182 TYR cc_start: 0.6831 (t80) cc_final: 0.5931 (t80) REVERT: D 1104 LYS cc_start: 0.7811 (mmpt) cc_final: 0.7559 (tppt) REVERT: D 1105 MET cc_start: 0.6137 (mtt) cc_final: 0.5831 (mtt) outliers start: 1 outliers final: 1 residues processed: 602 average time/residue: 0.4940 time to fit residues: 488.7751 Evaluate side-chains 461 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 460 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 363 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 289 optimal weight: 7.9990 chunk 279 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 427 optimal weight: 0.9990 chunk 342 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN ** 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 964 ASN ** B1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 519 HIS C 602 GLN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1371 ASN D 30 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN ** D1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.180198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.153139 restraints weight = 71106.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.151920 restraints weight = 94221.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.154201 restraints weight = 76344.970| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36050 Z= 0.139 Angle : 0.648 9.286 48828 Z= 0.330 Chirality : 0.046 0.269 5596 Planarity : 0.004 0.049 6294 Dihedral : 5.366 24.962 4816 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.65 % Favored : 90.32 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.12), residues: 4454 helix: -1.12 (0.15), residues: 1076 sheet: -1.39 (0.16), residues: 984 loop : -2.78 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 726 HIS 0.013 0.001 HIS D 789 PHE 0.023 0.002 PHE A1355 TYR 0.016 0.001 TYR D1048 ARG 0.011 0.000 ARG A 616 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 883) hydrogen bonds : angle 5.67096 ( 2352) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.84218 ( 8) covalent geometry : bond 0.00321 (36046) covalent geometry : angle 0.64823 (48820) ********************** 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 590 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 589 time to evaluate : 3.951 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: A 85 MET cc_start: 0.1277 (tpt) cc_final: -0.0461 (ttm) REVERT: A 155 MET cc_start: 0.1614 (ttt) cc_final: 0.1193 (tpt) REVERT: A 572 MET cc_start: 0.7856 (ptp) cc_final: 0.7537 (ptp) REVERT: A 726 TRP cc_start: 0.7115 (m-10) cc_final: 0.5991 (m100) REVERT: A 753 GLN cc_start: 0.7545 (tt0) cc_final: 0.6728 (tp-100) REVERT: A 773 GLN cc_start: 0.7629 (pp30) cc_final: 0.6749 (mp10) REVERT: A 791 LYS cc_start: 0.7899 (mmtm) cc_final: 0.7492 (mmmt) REVERT: A 1166 MET cc_start: 0.1969 (mmm) cc_final: 0.0038 (ptm) REVERT: A 1235 ASP cc_start: 0.7083 (m-30) cc_final: 0.6606 (t70) REVERT: B 182 TYR cc_start: 0.6769 (t80) cc_final: 0.5868 (t80) REVERT: B 449 MET cc_start: 0.1820 (mmm) cc_final: 0.0459 (mmt) REVERT: B 814 LEU cc_start: 0.7401 (mm) cc_final: 0.7188 (mm) REVERT: B 879 LYS cc_start: 0.6246 (tppt) cc_final: 0.5952 (mmmt) REVERT: B 925 ASP cc_start: 0.7573 (t0) cc_final: 0.6925 (p0) REVERT: B 989 ARG cc_start: 0.7902 (ptm160) cc_final: 0.6835 (ttp-170) REVERT: B 1014 MET cc_start: 0.5195 (mmt) cc_final: 0.4932 (mmm) REVERT: B 1097 PHE cc_start: 0.6380 (t80) cc_final: 0.6166 (t80) REVERT: B 1105 MET cc_start: 0.5851 (mtt) cc_final: 0.5344 (mtt) REVERT: C 85 MET cc_start: 0.1314 (tpt) cc_final: -0.0460 (ttm) REVERT: C 357 MET cc_start: 0.5741 (mmm) cc_final: 0.5465 (mmm) REVERT: C 399 LYS cc_start: 0.6969 (tptp) cc_final: 0.6676 (tptt) REVERT: C 571 MET cc_start: 0.8063 (mmt) cc_final: 0.7856 (tpt) REVERT: C 572 MET cc_start: 0.7865 (ptp) cc_final: 0.7565 (ptp) REVERT: C 753 GLN cc_start: 0.7612 (tt0) cc_final: 0.6721 (tp-100) REVERT: C 773 GLN cc_start: 0.7723 (pp30) cc_final: 0.7353 (pp30) REVERT: C 1013 ARG cc_start: 0.7430 (ttm110) cc_final: 0.7186 (ttm170) REVERT: C 1166 MET cc_start: 0.1996 (mmm) cc_final: 0.0108 (ptm) REVERT: C 1223 TYR cc_start: 0.7710 (m-10) cc_final: 0.7312 (m-10) REVERT: C 1345 ILE cc_start: 0.6057 (mp) cc_final: 0.5304 (mt) REVERT: D 182 TYR cc_start: 0.6897 (t80) cc_final: 0.5983 (t80) REVERT: D 606 LEU cc_start: 0.6775 (mm) cc_final: 0.6556 (mm) REVERT: D 679 MET cc_start: 0.4177 (ppp) cc_final: 0.3946 (ppp) REVERT: D 1014 MET cc_start: 0.3657 (tpt) cc_final: 0.2766 (tpt) REVERT: D 1097 PHE cc_start: 0.6174 (t80) cc_final: 0.5853 (t80) REVERT: D 1105 MET cc_start: 0.6063 (mtt) cc_final: 0.5822 (mtt) outliers start: 1 outliers final: 0 residues processed: 590 average time/residue: 0.4766 time to fit residues: 462.1122 Evaluate side-chains 463 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 184 optimal weight: 5.9990 chunk 384 optimal weight: 0.0980 chunk 188 optimal weight: 2.9990 chunk 371 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 400 optimal weight: 20.0000 chunk 410 optimal weight: 6.9990 chunk 345 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN A 785 GLN A 788 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 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 964 ASN B 978 GLN ** B1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 785 GLN C 788 GLN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN D 759 GLN ** D1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.175516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.147053 restraints weight = 71552.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.144757 restraints weight = 92828.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.146894 restraints weight = 79581.637| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 36050 Z= 0.210 Angle : 0.741 13.496 48828 Z= 0.381 Chirality : 0.049 0.279 5596 Planarity : 0.005 0.054 6294 Dihedral : 5.842 27.089 4816 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.94 % Favored : 88.01 % Rotamer: Outliers : 0.03 % Allowed : 0.51 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.12), residues: 4454 helix: -1.48 (0.15), residues: 1080 sheet: -1.59 (0.16), residues: 1012 loop : -2.90 (0.11), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 610 HIS 0.012 0.001 HIS B 789 PHE 0.024 0.002 PHE B1088 TYR 0.024 0.002 TYR D 58 ARG 0.016 0.001 ARG C 616 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 883) hydrogen bonds : angle 6.16068 ( 2352) SS BOND : bond 0.00614 ( 4) SS BOND : angle 1.12132 ( 8) covalent geometry : bond 0.00479 (36046) covalent geometry : angle 0.74097 (48820) =============================================================================== Job complete usr+sys time: 12786.49 seconds wall clock time: 221 minutes 41.27 seconds (13301.27 seconds total)