Starting phenix.real_space_refine on Mon Apr 15 17:28:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7b_31765/04_2024/7v7b_31765.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7b_31765/04_2024/7v7b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7b_31765/04_2024/7v7b_31765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7b_31765/04_2024/7v7b_31765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7b_31765/04_2024/7v7b_31765.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7b_31765/04_2024/7v7b_31765.pdb" } 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 Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 1018": "NH1" <-> "NH2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A ARG 1053": "NH1" <-> "NH2" Residue "A PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "B PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 842": "NH1" <-> "NH2" Residue "C ARG 1018": "NH1" <-> "NH2" Residue "C ARG 1043": "NH1" <-> "NH2" Residue "C ARG 1053": "NH1" <-> "NH2" Residue "C PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 722": "NH1" <-> "NH2" Residue "D PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35366 Number of models: 1 Model: "" Number of chains: 4 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 Chain: "C" 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: "D" 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 Time building chain proxies: 18.51, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 12.70 Conformation dependent library (CDL) restraints added in 6.2 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: 4.95 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: 17.70 Time building geometry restraints manager: 13.89 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: 98.79 - 105.87: 762 105.87 - 112.94: 19305 112.94 - 120.02: 12809 120.02 - 127.10: 15578 127.10 - 134.17: 366 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 2.440 nonbonded pdb=" OG SER D 737 " pdb=" OD1 ASN D 790 " model vdw 2.217 2.440 nonbonded pdb=" OE1 GLU A1272 " pdb=" OH TYR A1342 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLU C1272 " pdb=" OH TYR C1342 " model vdw 2.269 2.440 nonbonded pdb=" O LEU C 592 " pdb=" OG SER C 595 " model vdw 2.275 2.440 ... (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 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: 1.540 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: 7.490 Check model and map are aligned: 0.540 Set scattering table: 0.360 Process input model: 95.670 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.090 ------------------------------------------------------------------------------- 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 36046 Z= 0.294 Angle : 0.916 11.106 48820 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 1103 time to evaluate : 4.243 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: 0.5348 time to fit residues: 919.8828 Evaluate side-chains 618 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 618 time to evaluate : 4.301 ------------------------------------------------------------------------------- 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: 8.9990 chunk 339 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 351 optimal weight: 6.9990 chunk 135 optimal weight: 0.4980 chunk 213 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 406 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS A 433 HIS A 497 ASN A 553 HIS A 687 ASN A 773 GLN A 788 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 708 GLN 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 788 GLN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 370 GLN ** 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 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 HIS ** D 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 ASN D 708 GLN 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: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 36046 Z= 0.279 Angle : 0.717 9.986 48820 Z= 0.375 Chirality : 0.046 0.151 5596 Planarity : 0.005 0.056 6294 Dihedral : 6.283 32.598 4816 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.50 % 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: -4.10 (0.11), residues: 4454 helix: -2.81 (0.12), residues: 1012 sheet: -2.06 (0.16), residues: 994 loop : -3.05 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 447 HIS 0.008 0.002 HIS C 531 PHE 0.021 0.002 PHE A1301 TYR 0.027 0.002 TYR C1223 ARG 0.006 0.001 ARG D1102 *********************** 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 743 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 741 time to evaluate : 4.062 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: 0.4263 (t0) cc_final: 0.4031 (m-30) REVERT: A 85 MET cc_start: 0.0778 (tpt) cc_final: -0.1133 (ttm) REVERT: A 350 LEU cc_start: 0.8628 (mt) cc_final: 0.8071 (tp) REVERT: A 357 MET cc_start: 0.5830 (mmm) cc_final: 0.5606 (mmm) REVERT: A 515 GLN cc_start: 0.7293 (tt0) cc_final: 0.6984 (mm110) REVERT: A 616 ARG cc_start: 0.6951 (ptt-90) cc_final: 0.5810 (ptm-80) REVERT: A 773 GLN cc_start: 0.7746 (tm130) cc_final: 0.7070 (mp10) REVERT: A 814 GLU cc_start: 0.8228 (tp30) cc_final: 0.8012 (tp30) REVERT: A 1109 MET cc_start: 0.6378 (ptp) cc_final: 0.6161 (ptt) REVERT: A 1166 MET cc_start: 0.0667 (mmm) cc_final: -0.0156 (ptm) REVERT: A 1186 LYS cc_start: 0.5453 (mmmt) cc_final: 0.4718 (mmmm) REVERT: A 1288 LEU cc_start: 0.8309 (mp) cc_final: 0.7957 (tt) REVERT: A 1304 THR cc_start: 0.7521 (p) cc_final: 0.7110 (t) REVERT: B 182 TYR cc_start: 0.6991 (t80) cc_final: 0.6138 (t80) REVERT: B 213 GLU cc_start: 0.8269 (tt0) cc_final: 0.7923 (mt-10) REVERT: B 679 MET cc_start: 0.5324 (mmm) cc_final: 0.4624 (tmm) REVERT: B 723 LYS cc_start: 0.7193 (mttm) cc_final: 0.6498 (mmtp) REVERT: B 973 ASN cc_start: 0.8278 (m-40) cc_final: 0.7778 (m-40) REVERT: B 1114 TYR cc_start: 0.5898 (t80) cc_final: 0.5439 (t80) REVERT: C 9 ASP cc_start: 0.4253 (t0) cc_final: 0.4027 (m-30) REVERT: C 85 MET cc_start: 0.0702 (tpt) cc_final: -0.1189 (ttm) REVERT: C 350 LEU cc_start: 0.8644 (mt) cc_final: 0.8079 (tp) REVERT: C 357 MET cc_start: 0.5822 (mmm) cc_final: 0.5607 (mmm) REVERT: C 515 GLN cc_start: 0.7292 (tt0) cc_final: 0.6973 (mm110) REVERT: C 616 ARG cc_start: 0.6940 (ptt-90) cc_final: 0.5805 (ptm-80) REVERT: C 773 GLN cc_start: 0.7679 (tm130) cc_final: 0.7088 (mp10) REVERT: C 814 GLU cc_start: 0.8119 (tp30) cc_final: 0.7848 (tp30) REVERT: C 1109 MET cc_start: 0.6391 (ptp) cc_final: 0.6157 (ptt) REVERT: C 1166 MET cc_start: 0.0667 (mmm) cc_final: -0.0165 (ptm) REVERT: C 1186 LYS cc_start: 0.5458 (mmmt) cc_final: 0.4693 (mmmm) REVERT: C 1223 TYR cc_start: 0.7570 (m-80) cc_final: 0.7348 (t80) REVERT: C 1288 LEU cc_start: 0.8292 (mp) cc_final: 0.7980 (tt) REVERT: C 1304 THR cc_start: 0.7604 (p) cc_final: 0.7219 (t) REVERT: D 141 LYS cc_start: 0.7802 (mttt) cc_final: 0.7452 (mttm) REVERT: D 182 TYR cc_start: 0.7089 (t80) cc_final: 0.6106 (t80) REVERT: D 213 GLU cc_start: 0.8154 (tt0) cc_final: 0.7884 (tt0) REVERT: D 236 SER cc_start: 0.9002 (p) cc_final: 0.8374 (p) REVERT: D 606 LEU cc_start: 0.6610 (mm) cc_final: 0.6317 (mt) REVERT: D 679 MET cc_start: 0.5633 (mmm) cc_final: 0.4791 (tmm) REVERT: D 814 LEU cc_start: 0.7055 (mm) cc_final: 0.6851 (mm) REVERT: D 916 THR cc_start: 0.7961 (p) cc_final: 0.7614 (t) REVERT: D 973 ASN cc_start: 0.8238 (m-40) cc_final: 0.7813 (m-40) REVERT: D 1114 TYR cc_start: 0.6140 (t80) cc_final: 0.5804 (t80) outliers start: 2 outliers final: 2 residues processed: 743 average time/residue: 0.5345 time to fit residues: 637.3660 Evaluate side-chains 523 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 521 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 226 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 407 optimal weight: 6.9990 chunk 440 optimal weight: 0.2980 chunk 362 optimal weight: 8.9990 chunk 404 optimal weight: 40.0000 chunk 138 optimal weight: 7.9990 chunk 326 optimal weight: 0.0570 overall best weight: 2.2704 ------------------------------------------------------------------------------- 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 637 GLN A 720 HIS ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS A1201 HIS ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 370 GLN B 372 GLN B 439 ASN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B 727 GLN B 759 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 637 GLN C 720 HIS ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 HIS C1201 HIS ** C1259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 D 708 GLN D 727 GLN D 759 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36046 Z= 0.212 Angle : 0.632 9.412 48820 Z= 0.330 Chirality : 0.045 0.251 5596 Planarity : 0.005 0.053 6294 Dihedral : 5.842 30.374 4816 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % 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 : 0.05 % 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: -3.68 (0.11), residues: 4454 helix: -2.16 (0.14), residues: 1034 sheet: -1.85 (0.16), residues: 1034 loop : -2.90 (0.11), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 135 HIS 0.006 0.001 HIS C 531 PHE 0.021 0.002 PHE A1230 TYR 0.013 0.001 TYR A1131 ARG 0.005 0.000 ARG C 772 *********************** 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 684 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 684 time to evaluate : 3.976 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 85 MET cc_start: 0.2114 (tpt) cc_final: 0.0397 (ttm) REVERT: A 350 LEU cc_start: 0.8655 (mt) cc_final: 0.8033 (tp) REVERT: A 773 GLN cc_start: 0.7418 (pp30) cc_final: 0.7170 (mp10) REVERT: A 1166 MET cc_start: 0.0629 (mmm) cc_final: -0.0315 (ptm) REVERT: A 1186 LYS cc_start: 0.5599 (mmmt) cc_final: 0.5131 (mmmm) REVERT: A 1288 LEU cc_start: 0.8262 (mp) cc_final: 0.7914 (tt) REVERT: A 1304 THR cc_start: 0.7423 (p) cc_final: 0.7071 (t) REVERT: B 182 TYR cc_start: 0.6879 (t80) cc_final: 0.6102 (t80) REVERT: B 213 GLU cc_start: 0.8237 (tt0) cc_final: 0.7940 (mt-10) REVERT: B 355 ASN cc_start: 0.8814 (t0) cc_final: 0.8232 (t0) REVERT: B 449 MET cc_start: 0.1152 (mmm) cc_final: 0.0739 (mmp) REVERT: B 679 MET cc_start: 0.4463 (mmm) cc_final: 0.4213 (tmm) REVERT: B 835 MET cc_start: 0.7396 (mmm) cc_final: 0.6659 (mmt) REVERT: B 973 ASN cc_start: 0.8075 (m-40) cc_final: 0.7657 (m-40) REVERT: B 1104 LYS cc_start: 0.7727 (mmpt) cc_final: 0.7267 (tppt) REVERT: B 1114 TYR cc_start: 0.5884 (t80) cc_final: 0.5584 (t80) REVERT: C 85 MET cc_start: 0.2070 (tpt) cc_final: 0.0382 (ttm) REVERT: C 350 LEU cc_start: 0.8662 (mt) cc_final: 0.8046 (tp) REVERT: C 357 MET cc_start: 0.5905 (mmm) cc_final: 0.5687 (mmm) REVERT: C 602 GLN cc_start: 0.8253 (tp-100) cc_final: 0.7712 (tp-100) REVERT: C 773 GLN cc_start: 0.7422 (pp30) cc_final: 0.7153 (mp10) REVERT: C 1166 MET cc_start: 0.0619 (mmm) cc_final: -0.0341 (ptm) REVERT: C 1186 LYS cc_start: 0.5565 (mmmt) cc_final: 0.5137 (mmmm) REVERT: C 1288 LEU cc_start: 0.8317 (mp) cc_final: 0.7962 (tt) REVERT: C 1304 THR cc_start: 0.7339 (p) cc_final: 0.7016 (t) REVERT: D 182 TYR cc_start: 0.7125 (t80) cc_final: 0.6250 (t80) REVERT: D 213 GLU cc_start: 0.8138 (tt0) cc_final: 0.7789 (tt0) REVERT: D 236 SER cc_start: 0.8976 (p) cc_final: 0.8292 (p) REVERT: D 355 ASN cc_start: 0.8811 (t0) cc_final: 0.8238 (t0) REVERT: D 449 MET cc_start: 0.0861 (mmm) cc_final: 0.0579 (mmp) REVERT: D 679 MET cc_start: 0.5563 (mmm) cc_final: 0.4939 (tmm) REVERT: D 973 ASN cc_start: 0.7926 (m-40) cc_final: 0.7359 (m-40) REVERT: D 1104 LYS cc_start: 0.7714 (mmpt) cc_final: 0.7366 (tppt) REVERT: D 1114 TYR cc_start: 0.6220 (t80) cc_final: 0.5975 (t80) outliers start: 0 outliers final: 0 residues processed: 684 average time/residue: 0.4820 time to fit residues: 535.2881 Evaluate side-chains 504 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 402 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 409 optimal weight: 10.0000 chunk 433 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 387 optimal weight: 30.0000 chunk 116 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS A 637 GLN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 343 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS C 602 GLN C 637 GLN ** C 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 GLN ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 HIS ** C1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** 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 439 ASN D 708 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 759 GLN D 803 HIS ** D 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 36046 Z= 0.434 Angle : 0.830 8.902 48820 Z= 0.432 Chirality : 0.050 0.186 5596 Planarity : 0.006 0.066 6294 Dihedral : 6.630 28.743 4816 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: -4.01 (0.11), residues: 4454 helix: -2.44 (0.13), residues: 1042 sheet: -2.08 (0.16), residues: 996 loop : -3.09 (0.11), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP C 135 HIS 0.012 0.002 HIS A 802 PHE 0.031 0.003 PHE A1301 TYR 0.022 0.003 TYR D1048 ARG 0.007 0.001 ARG D1102 *********************** 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 610 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 610 time to evaluate : 4.260 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: 0.1625 (tpt) cc_final: -0.0174 (ttm) REVERT: A 350 LEU cc_start: 0.8637 (mt) cc_final: 0.7774 (tp) REVERT: A 399 LYS cc_start: 0.7502 (tptp) cc_final: 0.6808 (tptt) REVERT: A 1109 MET cc_start: 0.6478 (ptp) cc_final: 0.6250 (ptt) REVERT: A 1166 MET cc_start: 0.1072 (mmm) cc_final: -0.0086 (ptm) REVERT: A 1180 HIS cc_start: 0.3203 (t-90) cc_final: 0.2947 (p90) REVERT: A 1235 ASP cc_start: 0.7468 (m-30) cc_final: 0.6868 (t70) REVERT: A 1259 ASN cc_start: 0.7192 (t0) cc_final: 0.6681 (t0) REVERT: A 1288 LEU cc_start: 0.8469 (mp) cc_final: 0.8209 (tt) REVERT: A 1304 THR cc_start: 0.7521 (p) cc_final: 0.7310 (t) REVERT: B 182 TYR cc_start: 0.6936 (t80) cc_final: 0.6013 (t80) REVERT: B 213 GLU cc_start: 0.8323 (tt0) cc_final: 0.8089 (mt-10) REVERT: B 236 SER cc_start: 0.9085 (p) cc_final: 0.8673 (p) REVERT: B 449 MET cc_start: 0.1748 (mmm) cc_final: 0.0318 (mmt) REVERT: B 679 MET cc_start: 0.5228 (mmm) cc_final: 0.4604 (ppp) REVERT: B 722 ARG cc_start: 0.6388 (mmp-170) cc_final: 0.6112 (mmp-170) REVERT: B 902 GLU cc_start: 0.7872 (tt0) cc_final: 0.7615 (tt0) REVERT: B 1014 MET cc_start: 0.5360 (tpt) cc_final: 0.4540 (tpt) REVERT: B 1104 LYS cc_start: 0.7715 (mmpt) cc_final: 0.7423 (tppt) REVERT: C 85 MET cc_start: 0.1590 (tpt) cc_final: -0.0196 (ttm) REVERT: C 350 LEU cc_start: 0.8654 (mt) cc_final: 0.7838 (tp) REVERT: C 357 MET cc_start: 0.5997 (mmm) cc_final: 0.5691 (mmm) REVERT: C 399 LYS cc_start: 0.7632 (tptp) cc_final: 0.6936 (tptt) REVERT: C 1109 MET cc_start: 0.6485 (ptp) cc_final: 0.6260 (ptt) REVERT: C 1166 MET cc_start: 0.0916 (mmm) cc_final: -0.0182 (ptm) REVERT: C 1180 HIS cc_start: 0.3149 (t-90) cc_final: 0.2915 (p90) REVERT: C 1235 ASP cc_start: 0.7391 (m-30) cc_final: 0.6861 (t70) REVERT: C 1288 LEU cc_start: 0.8487 (mp) cc_final: 0.8251 (tt) REVERT: D 182 TYR cc_start: 0.7127 (t80) cc_final: 0.6177 (t80) REVERT: D 679 MET cc_start: 0.5770 (mmm) cc_final: 0.5032 (ppp) REVERT: D 722 ARG cc_start: 0.6427 (mmp-170) cc_final: 0.6039 (mmp-170) REVERT: D 811 GLU cc_start: 0.6925 (tt0) cc_final: 0.6594 (tt0) REVERT: D 835 MET cc_start: 0.8130 (mmm) cc_final: 0.7689 (mmm) REVERT: D 1014 MET cc_start: 0.4296 (tpt) cc_final: 0.3642 (tpt) REVERT: D 1092 ASP cc_start: 0.8445 (m-30) cc_final: 0.8238 (m-30) REVERT: D 1104 LYS cc_start: 0.7766 (mmpt) cc_final: 0.7490 (tppt) REVERT: D 1105 MET cc_start: 0.6354 (mtt) cc_final: 0.5625 (mtt) outliers start: 0 outliers final: 0 residues processed: 610 average time/residue: 0.5024 time to fit residues: 499.9751 Evaluate side-chains 448 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 448 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 360 optimal weight: 0.5980 chunk 245 optimal weight: 4.9990 chunk 6 optimal weight: 0.0020 chunk 322 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 369 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 221 optimal weight: 7.9990 chunk 388 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 183 GLN A 193 ASN ** 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 520 GLN B 531 HIS ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B 727 GLN B 731 GLN B 759 GLN B1034 ASN C 183 GLN C 193 ASN C 602 GLN ** 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 520 GLN D 531 HIS D 708 GLN D 731 GLN D 759 GLN ** D 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1034 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36046 Z= 0.189 Angle : 0.623 7.495 48820 Z= 0.323 Chirality : 0.045 0.242 5596 Planarity : 0.004 0.052 6294 Dihedral : 5.833 26.823 4816 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.78 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -3.59 (0.11), residues: 4454 helix: -1.83 (0.14), residues: 1046 sheet: -1.88 (0.16), residues: 1040 loop : -2.95 (0.11), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 135 HIS 0.004 0.001 HIS A 802 PHE 0.017 0.002 PHE D1088 TYR 0.026 0.001 TYR B1048 ARG 0.005 0.000 ARG B 527 *********************** 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 625 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 4.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.1562 (tpt) cc_final: -0.0114 (ttm) REVERT: A 350 LEU cc_start: 0.8617 (mt) cc_final: 0.7970 (tp) REVERT: A 357 MET cc_start: 0.6248 (mmm) cc_final: 0.6030 (mmm) REVERT: A 1166 MET cc_start: 0.1080 (mmm) cc_final: -0.0171 (ptm) REVERT: A 1180 HIS cc_start: 0.3433 (t-90) cc_final: 0.3012 (p90) REVERT: A 1288 LEU cc_start: 0.8285 (mp) cc_final: 0.8050 (tt) REVERT: A 1304 THR cc_start: 0.7466 (p) cc_final: 0.7184 (t) REVERT: B 64 MET cc_start: 0.8315 (pmm) cc_final: 0.7721 (pmm) REVERT: B 133 LEU cc_start: 0.7312 (mt) cc_final: 0.7111 (mt) REVERT: B 135 LEU cc_start: 0.7824 (mt) cc_final: 0.7619 (mt) REVERT: B 182 TYR cc_start: 0.6852 (t80) cc_final: 0.5918 (t80) REVERT: B 213 GLU cc_start: 0.8248 (tt0) cc_final: 0.8006 (mt-10) REVERT: B 236 SER cc_start: 0.9024 (p) cc_final: 0.8658 (p) REVERT: B 355 ASN cc_start: 0.8899 (t0) cc_final: 0.8431 (t0) REVERT: B 679 MET cc_start: 0.5075 (mmm) cc_final: 0.4669 (ppp) REVERT: B 722 ARG cc_start: 0.6478 (mmp-170) cc_final: 0.5966 (mmp-170) REVERT: B 835 MET cc_start: 0.7918 (mmm) cc_final: 0.7583 (mmp) REVERT: B 1014 MET cc_start: 0.4760 (tpt) cc_final: 0.4447 (tpt) REVERT: B 1104 LYS cc_start: 0.7770 (mmpt) cc_final: 0.7458 (tppt) REVERT: B 1105 MET cc_start: 0.5897 (mtt) cc_final: 0.5352 (mtt) REVERT: B 1114 TYR cc_start: 0.6062 (t80) cc_final: 0.5504 (t80) REVERT: C 85 MET cc_start: 0.1579 (tpt) cc_final: -0.0070 (ttm) REVERT: C 350 LEU cc_start: 0.8655 (mt) cc_final: 0.7904 (tp) REVERT: C 402 GLU cc_start: 0.6952 (mt-10) cc_final: 0.5549 (tp30) REVERT: C 572 MET cc_start: 0.7543 (ptp) cc_final: 0.6924 (ptp) REVERT: C 1166 MET cc_start: 0.1081 (mmm) cc_final: -0.0154 (ptm) REVERT: C 1180 HIS cc_start: 0.3385 (t-90) cc_final: 0.2911 (p90) REVERT: C 1288 LEU cc_start: 0.8301 (mp) cc_final: 0.8055 (tt) REVERT: C 1304 THR cc_start: 0.7382 (p) cc_final: 0.7122 (t) REVERT: D 182 TYR cc_start: 0.6992 (t80) cc_final: 0.6012 (t80) REVERT: D 284 LEU cc_start: 0.7302 (mp) cc_final: 0.6990 (mt) REVERT: D 355 ASN cc_start: 0.8981 (t0) cc_final: 0.8529 (t0) REVERT: D 679 MET cc_start: 0.5768 (mmm) cc_final: 0.5055 (tmm) REVERT: D 722 ARG cc_start: 0.6428 (mmp-170) cc_final: 0.5972 (mmp-170) REVERT: D 1014 MET cc_start: 0.3530 (tpt) cc_final: 0.3012 (tpt) REVERT: D 1104 LYS cc_start: 0.7692 (mmpt) cc_final: 0.7407 (tppt) REVERT: D 1105 MET cc_start: 0.6376 (mtt) cc_final: 0.5638 (mtt) outliers start: 0 outliers final: 0 residues processed: 625 average time/residue: 0.4836 time to fit residues: 491.7867 Evaluate side-chains 473 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 4.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 145 optimal weight: 0.4980 chunk 389 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 254 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 433 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 GLN ** 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 439 ASN B 470 GLN B 520 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B1034 ASN B1077 HIS C 102 ASN C 602 GLN C 637 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** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36046 Z= 0.183 Angle : 0.609 7.341 48820 Z= 0.313 Chirality : 0.044 0.176 5596 Planarity : 0.004 0.050 6294 Dihedral : 5.500 26.448 4816 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.65 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: -3.39 (0.11), residues: 4454 helix: -1.60 (0.15), residues: 1068 sheet: -1.65 (0.16), residues: 1000 loop : -2.90 (0.11), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP C 135 HIS 0.005 0.001 HIS A 459 PHE 0.022 0.001 PHE D1097 TYR 0.027 0.001 TYR D1048 ARG 0.012 0.000 ARG D 111 *********************** 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 613 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 613 time to evaluate : 4.412 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: 0.1666 (tpt) cc_final: -0.0025 (ttm) REVERT: A 350 LEU cc_start: 0.8610 (mt) cc_final: 0.7947 (tp) REVERT: A 572 MET cc_start: 0.7645 (ptp) cc_final: 0.7161 (ptp) REVERT: A 746 MET cc_start: 0.7589 (tmm) cc_final: 0.7293 (ttt) REVERT: A 753 GLN cc_start: 0.7055 (tt0) cc_final: 0.6444 (tp-100) REVERT: A 773 GLN cc_start: 0.7607 (pp30) cc_final: 0.6861 (mp10) REVERT: A 1013 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7268 (mtm180) REVERT: A 1166 MET cc_start: 0.1255 (mmm) cc_final: -0.0152 (ptm) REVERT: A 1288 LEU cc_start: 0.8278 (mp) cc_final: 0.8036 (tt) REVERT: A 1304 THR cc_start: 0.7646 (p) cc_final: 0.7364 (t) REVERT: B 64 MET cc_start: 0.8257 (pmm) cc_final: 0.8042 (pmm) REVERT: B 182 TYR cc_start: 0.6794 (t80) cc_final: 0.5890 (t80) REVERT: B 208 LYS cc_start: 0.8227 (mttt) cc_final: 0.7734 (mmtm) REVERT: B 355 ASN cc_start: 0.8940 (t0) cc_final: 0.8475 (t0) REVERT: B 679 MET cc_start: 0.4841 (mmm) cc_final: 0.4535 (ppp) REVERT: B 722 ARG cc_start: 0.6393 (mmp-170) cc_final: 0.5956 (mmp-170) REVERT: B 1048 TYR cc_start: 0.7638 (t80) cc_final: 0.7233 (t80) REVERT: B 1097 PHE cc_start: 0.6406 (t80) cc_final: 0.5995 (t80) REVERT: B 1104 LYS cc_start: 0.7778 (mmpt) cc_final: 0.7469 (tppt) REVERT: B 1105 MET cc_start: 0.5962 (mtt) cc_final: 0.5555 (mtt) REVERT: B 1114 TYR cc_start: 0.6076 (t80) cc_final: 0.5695 (t80) REVERT: C 85 MET cc_start: 0.1612 (tpt) cc_final: -0.0042 (ttm) REVERT: C 350 LEU cc_start: 0.8619 (mt) cc_final: 0.7864 (tp) REVERT: C 402 GLU cc_start: 0.6637 (mt-10) cc_final: 0.5570 (tm-30) REVERT: C 572 MET cc_start: 0.7647 (ptp) cc_final: 0.7153 (ptp) REVERT: C 753 GLN cc_start: 0.7540 (mt0) cc_final: 0.7135 (tp-100) REVERT: C 773 GLN cc_start: 0.7564 (pp30) cc_final: 0.6835 (mp10) REVERT: C 1166 MET cc_start: 0.1251 (mmm) cc_final: -0.0149 (ptm) REVERT: C 1288 LEU cc_start: 0.8257 (mp) cc_final: 0.8051 (tt) REVERT: C 1304 THR cc_start: 0.7637 (p) cc_final: 0.7303 (t) REVERT: C 1345 ILE cc_start: 0.7180 (mp) cc_final: 0.6750 (mt) REVERT: D 130 MET cc_start: 0.6408 (ptt) cc_final: 0.6207 (ptm) REVERT: D 182 TYR cc_start: 0.7018 (t80) cc_final: 0.6024 (t80) REVERT: D 355 ASN cc_start: 0.8963 (t0) cc_final: 0.8580 (t0) REVERT: D 679 MET cc_start: 0.5989 (mmm) cc_final: 0.4810 (tmm) REVERT: D 989 ARG cc_start: 0.7709 (ptm160) cc_final: 0.7329 (ptm-80) REVERT: D 1014 MET cc_start: 0.3672 (tpt) cc_final: 0.3149 (tpt) REVERT: D 1097 PHE cc_start: 0.6445 (t80) cc_final: 0.6211 (t80) REVERT: D 1104 LYS cc_start: 0.7771 (mmpt) cc_final: 0.7529 (tppt) REVERT: D 1105 MET cc_start: 0.6254 (mtt) cc_final: 0.5681 (mtt) outliers start: 0 outliers final: 0 residues processed: 613 average time/residue: 0.4818 time to fit residues: 487.4856 Evaluate side-chains 470 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 417 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 431 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 263 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 519 HIS A 637 GLN ** 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 520 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B 727 GLN B 759 GLN B1034 ASN C 183 GLN C 519 HIS C 637 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** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36046 Z= 0.217 Angle : 0.633 8.648 48820 Z= 0.325 Chirality : 0.045 0.170 5596 Planarity : 0.004 0.051 6294 Dihedral : 5.510 26.693 4816 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.97 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.25 (0.12), residues: 4454 helix: -1.38 (0.15), residues: 1056 sheet: -1.70 (0.16), residues: 1014 loop : -2.80 (0.11), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 135 HIS 0.006 0.001 HIS D 240 PHE 0.020 0.002 PHE B1088 TYR 0.016 0.001 TYR B 837 ARG 0.008 0.000 ARG D 111 *********************** 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 601 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 4.310 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: A 85 MET cc_start: 0.1758 (tpt) cc_final: 0.0075 (ttm) REVERT: A 350 LEU cc_start: 0.8628 (mt) cc_final: 0.7901 (tp) REVERT: A 572 MET cc_start: 0.7765 (ptp) cc_final: 0.7219 (ptp) REVERT: A 1013 ARG cc_start: 0.7596 (ttm110) cc_final: 0.7187 (mtm180) REVERT: A 1166 MET cc_start: 0.1372 (mmm) cc_final: -0.0033 (ptm) REVERT: A 1180 HIS cc_start: 0.3637 (t-90) cc_final: 0.3046 (p90) REVERT: A 1235 ASP cc_start: 0.7333 (m-30) cc_final: 0.6785 (t70) REVERT: A 1288 LEU cc_start: 0.8331 (mp) cc_final: 0.8099 (tt) REVERT: A 1304 THR cc_start: 0.7736 (p) cc_final: 0.7426 (t) REVERT: B 182 TYR cc_start: 0.6833 (t80) cc_final: 0.5796 (t80) REVERT: B 200 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8187 (ttpp) REVERT: B 355 ASN cc_start: 0.8982 (t0) cc_final: 0.8471 (t0) REVERT: B 973 ASN cc_start: 0.7788 (m-40) cc_final: 0.7432 (m-40) REVERT: B 1048 TYR cc_start: 0.7579 (t80) cc_final: 0.7218 (t80) REVERT: B 1097 PHE cc_start: 0.6486 (t80) cc_final: 0.6177 (t80) REVERT: B 1104 LYS cc_start: 0.7747 (mmpt) cc_final: 0.7540 (tppt) REVERT: B 1114 TYR cc_start: 0.6230 (t80) cc_final: 0.5787 (t80) REVERT: C 85 MET cc_start: 0.1712 (tpt) cc_final: 0.0060 (ttm) REVERT: C 350 LEU cc_start: 0.8619 (mt) cc_final: 0.7776 (tp) REVERT: C 357 MET cc_start: 0.6104 (mmm) cc_final: 0.5545 (mmm) REVERT: C 572 MET cc_start: 0.7775 (ptp) cc_final: 0.7233 (ptp) REVERT: C 753 GLN cc_start: 0.7583 (mt0) cc_final: 0.7158 (tp-100) REVERT: C 843 ILE cc_start: 0.7947 (mm) cc_final: 0.7681 (mt) REVERT: C 1013 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7407 (mtm180) REVERT: C 1153 SER cc_start: 0.2930 (p) cc_final: 0.2707 (m) REVERT: C 1166 MET cc_start: 0.1412 (mmm) cc_final: -0.0040 (ptm) REVERT: C 1180 HIS cc_start: 0.3555 (t-90) cc_final: 0.2966 (p90) REVERT: C 1235 ASP cc_start: 0.7262 (m-30) cc_final: 0.6693 (t70) REVERT: C 1288 LEU cc_start: 0.8336 (mp) cc_final: 0.8131 (tt) REVERT: C 1304 THR cc_start: 0.7702 (p) cc_final: 0.7387 (t) REVERT: D 182 TYR cc_start: 0.7034 (t80) cc_final: 0.5995 (t80) REVERT: D 341 ASN cc_start: 0.8925 (t0) cc_final: 0.8711 (t0) REVERT: D 355 ASN cc_start: 0.8997 (t0) cc_final: 0.8613 (t0) REVERT: D 679 MET cc_start: 0.5841 (mmm) cc_final: 0.4942 (tmm) REVERT: D 989 ARG cc_start: 0.7812 (ptm160) cc_final: 0.7409 (ptm-80) REVERT: D 1014 MET cc_start: 0.3210 (tpt) cc_final: 0.2866 (tpt) REVERT: D 1048 TYR cc_start: 0.7933 (t80) cc_final: 0.7569 (t80) REVERT: D 1097 PHE cc_start: 0.6549 (t80) cc_final: 0.6307 (t80) REVERT: D 1104 LYS cc_start: 0.7751 (mmpt) cc_final: 0.7510 (tppt) REVERT: D 1105 MET cc_start: 0.6379 (mtt) cc_final: 0.5838 (mtt) outliers start: 0 outliers final: 0 residues processed: 601 average time/residue: 0.4868 time to fit residues: 481.2308 Evaluate side-chains 455 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 267 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 213 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 339 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 602 GLN A 637 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 HIS ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN C 519 HIS C 609 ASN C 637 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** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN D 727 GLN D 778 HIS D 964 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36046 Z= 0.228 Angle : 0.640 9.529 48820 Z= 0.328 Chirality : 0.045 0.236 5596 Planarity : 0.004 0.058 6294 Dihedral : 5.541 26.671 4816 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.24 % Favored : 89.72 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -3.20 (0.12), residues: 4454 helix: -1.31 (0.15), residues: 1068 sheet: -1.74 (0.16), residues: 1032 loop : -2.76 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP C 135 HIS 0.006 0.001 HIS D 240 PHE 0.021 0.002 PHE B1088 TYR 0.015 0.002 TYR B1048 ARG 0.013 0.001 ARG B 111 *********************** 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 592 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 592 time to evaluate : 4.381 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: A 85 MET cc_start: 0.1893 (tpt) cc_final: 0.0237 (ttm) REVERT: A 350 LEU cc_start: 0.8601 (mt) cc_final: 0.7891 (tp) REVERT: A 572 MET cc_start: 0.7886 (ptp) cc_final: 0.7416 (ptp) REVERT: A 773 GLN cc_start: 0.7767 (pp30) cc_final: 0.7370 (pp30) REVERT: A 1013 ARG cc_start: 0.7640 (ttm110) cc_final: 0.7185 (mtt90) REVERT: A 1166 MET cc_start: 0.1932 (mmm) cc_final: 0.0087 (ptm) REVERT: A 1180 HIS cc_start: 0.4020 (t-90) cc_final: 0.3060 (p90) REVERT: A 1235 ASP cc_start: 0.7389 (m-30) cc_final: 0.6738 (t70) REVERT: A 1259 ASN cc_start: 0.7043 (t0) cc_final: 0.6575 (t0) REVERT: A 1260 MET cc_start: 0.1971 (ptt) cc_final: 0.1608 (ptt) REVERT: A 1288 LEU cc_start: 0.8314 (mp) cc_final: 0.8068 (tt) REVERT: A 1304 THR cc_start: 0.7822 (p) cc_final: 0.7496 (t) REVERT: B 182 TYR cc_start: 0.6864 (t80) cc_final: 0.5829 (t80) REVERT: B 200 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8186 (ttpp) REVERT: B 341 ASN cc_start: 0.8959 (t0) cc_final: 0.8755 (t0) REVERT: B 355 ASN cc_start: 0.8999 (t0) cc_final: 0.8508 (t0) REVERT: B 679 MET cc_start: 0.4301 (ppp) cc_final: 0.3921 (ppp) REVERT: B 835 MET cc_start: 0.7682 (mmm) cc_final: 0.6908 (mmt) REVERT: B 973 ASN cc_start: 0.7923 (m-40) cc_final: 0.7417 (m-40) REVERT: B 1048 TYR cc_start: 0.7684 (t80) cc_final: 0.7393 (t80) REVERT: B 1097 PHE cc_start: 0.6451 (t80) cc_final: 0.6127 (t80) REVERT: C 85 MET cc_start: 0.1844 (tpt) cc_final: 0.0228 (ttm) REVERT: C 350 LEU cc_start: 0.8629 (mt) cc_final: 0.7861 (tp) REVERT: C 572 MET cc_start: 0.7877 (ptp) cc_final: 0.7437 (ptp) REVERT: C 753 GLN cc_start: 0.7646 (mt0) cc_final: 0.7166 (tp-100) REVERT: C 773 GLN cc_start: 0.7697 (pp30) cc_final: 0.7266 (pp30) REVERT: C 1013 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7348 (mtm180) REVERT: C 1166 MET cc_start: 0.1899 (mmm) cc_final: 0.0056 (ptm) REVERT: C 1180 HIS cc_start: 0.3840 (t-90) cc_final: 0.2970 (p-80) REVERT: C 1235 ASP cc_start: 0.7344 (m-30) cc_final: 0.6736 (t70) REVERT: C 1288 LEU cc_start: 0.8365 (mp) cc_final: 0.8156 (tt) REVERT: C 1304 THR cc_start: 0.7783 (p) cc_final: 0.7485 (t) REVERT: D 182 TYR cc_start: 0.7013 (t80) cc_final: 0.5958 (t80) REVERT: D 355 ASN cc_start: 0.9043 (t0) cc_final: 0.8613 (t0) REVERT: D 606 LEU cc_start: 0.6831 (mm) cc_final: 0.6624 (mm) REVERT: D 811 GLU cc_start: 0.6654 (tt0) cc_final: 0.6375 (tt0) REVERT: D 835 MET cc_start: 0.7618 (mmm) cc_final: 0.7399 (mmp) REVERT: D 873 MET cc_start: 0.8513 (mtm) cc_final: 0.8074 (mtm) REVERT: D 989 ARG cc_start: 0.7857 (ptm160) cc_final: 0.7439 (ptm-80) REVERT: D 1014 MET cc_start: 0.3420 (tpt) cc_final: 0.2955 (tpt) REVERT: D 1048 TYR cc_start: 0.8068 (t80) cc_final: 0.7830 (t80) REVERT: D 1097 PHE cc_start: 0.6655 (t80) cc_final: 0.6302 (t80) REVERT: D 1104 LYS cc_start: 0.7766 (mmpt) cc_final: 0.7548 (tppt) REVERT: D 1105 MET cc_start: 0.6235 (mtt) cc_final: 0.5767 (mtt) outliers start: 0 outliers final: 0 residues processed: 592 average time/residue: 0.4786 time to fit residues: 467.2768 Evaluate side-chains 455 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 4.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 392 optimal weight: 7.9990 chunk 413 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 402 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 315 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 363 optimal weight: 7.9990 chunk 380 optimal weight: 0.9980 chunk 400 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 602 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 520 GLN B 524 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B 727 GLN B 759 GLN C 183 GLN C 519 HIS ** 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 372 GLN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN D 727 GLN D 759 GLN ** D 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 36046 Z= 0.395 Angle : 0.802 10.643 48820 Z= 0.415 Chirality : 0.050 0.248 5596 Planarity : 0.005 0.069 6294 Dihedral : 6.364 29.353 4816 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.11 % Favored : 86.84 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.11), residues: 4454 helix: -1.86 (0.14), residues: 1060 sheet: -1.89 (0.15), residues: 1024 loop : -3.05 (0.11), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.004 TRP C 135 HIS 0.012 0.002 HIS B 522 PHE 0.028 0.003 PHE B1088 TYR 0.023 0.002 TYR D 837 ARG 0.060 0.001 ARG C 616 *********************** 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 562 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 3.986 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: A 85 MET cc_start: 0.1979 (tpt) cc_final: 0.0241 (ttm) REVERT: A 183 GLN cc_start: 0.6812 (mt0) cc_final: 0.6456 (mt0) REVERT: A 773 GLN cc_start: 0.7963 (pp30) cc_final: 0.7539 (pp30) REVERT: A 1013 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7166 (mtt90) REVERT: A 1166 MET cc_start: 0.2096 (mmm) cc_final: 0.0049 (ptm) REVERT: A 1186 LYS cc_start: 0.6303 (mmmt) cc_final: 0.6082 (mmmm) REVERT: A 1259 ASN cc_start: 0.6835 (t0) cc_final: 0.6627 (t0) REVERT: B 182 TYR cc_start: 0.6899 (t80) cc_final: 0.5884 (t80) REVERT: B 200 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8247 (ttpp) REVERT: B 355 ASN cc_start: 0.9102 (t0) cc_final: 0.8692 (t0) REVERT: B 722 ARG cc_start: 0.6524 (mmp-170) cc_final: 0.5993 (mmp-170) REVERT: B 811 GLU cc_start: 0.6754 (tt0) cc_final: 0.6456 (tt0) REVERT: B 835 MET cc_start: 0.7741 (mmm) cc_final: 0.7222 (mmm) REVERT: B 973 ASN cc_start: 0.8190 (m-40) cc_final: 0.7149 (m-40) REVERT: B 989 ARG cc_start: 0.8022 (ptm160) cc_final: 0.7195 (ttp-170) REVERT: B 1097 PHE cc_start: 0.6689 (t80) cc_final: 0.6367 (t80) REVERT: C 85 MET cc_start: 0.1950 (tpt) cc_final: 0.0206 (ttm) REVERT: C 350 LEU cc_start: 0.8654 (mt) cc_final: 0.7869 (tp) REVERT: C 381 LEU cc_start: 0.7960 (mt) cc_final: 0.7661 (mt) REVERT: C 773 GLN cc_start: 0.7897 (pp30) cc_final: 0.7440 (pp30) REVERT: C 1013 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7174 (mtm180) REVERT: C 1166 MET cc_start: 0.2073 (mmm) cc_final: 0.0054 (ptm) REVERT: C 1335 ARG cc_start: 0.7645 (tpm170) cc_final: 0.6900 (ttm-80) REVERT: C 1345 ILE cc_start: 0.6604 (mp) cc_final: 0.6158 (mt) REVERT: D 182 TYR cc_start: 0.7060 (t80) cc_final: 0.5927 (t80) REVERT: D 355 ASN cc_start: 0.9107 (t0) cc_final: 0.8753 (t0) REVERT: D 606 LEU cc_start: 0.6979 (mm) cc_final: 0.6751 (mm) REVERT: D 873 MET cc_start: 0.8690 (mtm) cc_final: 0.8279 (mtm) REVERT: D 989 ARG cc_start: 0.7979 (ptm160) cc_final: 0.7036 (ttp-170) REVERT: D 1097 PHE cc_start: 0.6698 (t80) cc_final: 0.6387 (t80) REVERT: D 1105 MET cc_start: 0.6233 (mtt) cc_final: 0.6026 (mtp) REVERT: D 1114 TYR cc_start: 0.6111 (t80) cc_final: 0.5790 (t80) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.4944 time to fit residues: 457.3650 Evaluate side-chains 437 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 264 optimal weight: 5.9990 chunk 425 optimal weight: 1.9990 chunk 259 optimal weight: 10.0000 chunk 201 optimal weight: 0.5980 chunk 295 optimal weight: 6.9990 chunk 446 optimal weight: 8.9990 chunk 410 optimal weight: 0.7980 chunk 355 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 274 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 602 GLN ** 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 520 GLN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B 727 GLN ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** 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 470 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN D 727 GLN D 964 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36046 Z= 0.169 Angle : 0.642 11.356 48820 Z= 0.325 Chirality : 0.045 0.238 5596 Planarity : 0.004 0.063 6294 Dihedral : 5.549 24.918 4816 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.28 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % 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: -3.22 (0.12), residues: 4454 helix: -1.24 (0.15), residues: 1088 sheet: -1.77 (0.16), residues: 990 loop : -2.80 (0.11), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP C 135 HIS 0.006 0.001 HIS A1140 PHE 0.015 0.001 PHE D1097 TYR 0.040 0.002 TYR B1048 ARG 0.011 0.000 ARG B 111 ********************** 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 604 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 604 time to evaluate : 4.364 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: A 85 MET cc_start: 0.1704 (tpt) cc_final: 0.0021 (ttm) REVERT: A 350 LEU cc_start: 0.8822 (mt) cc_final: 0.8339 (tp) REVERT: A 753 GLN cc_start: 0.7304 (tt0) cc_final: 0.6815 (tp-100) REVERT: A 773 GLN cc_start: 0.7614 (pp30) cc_final: 0.7197 (pp30) REVERT: A 1013 ARG cc_start: 0.7490 (ttm110) cc_final: 0.6967 (mtt90) REVERT: A 1166 MET cc_start: 0.2044 (mmm) cc_final: 0.0039 (ptm) REVERT: A 1180 HIS cc_start: 0.4191 (t-90) cc_final: 0.2990 (p90) REVERT: A 1235 ASP cc_start: 0.7545 (m-30) cc_final: 0.6775 (t70) REVERT: A 1304 THR cc_start: 0.7759 (p) cc_final: 0.7473 (t) REVERT: B 102 THR cc_start: 0.7601 (m) cc_final: 0.7116 (p) REVERT: B 182 TYR cc_start: 0.6791 (t80) cc_final: 0.5746 (t80) REVERT: B 355 ASN cc_start: 0.8818 (t0) cc_final: 0.8574 (t0) REVERT: B 717 LEU cc_start: 0.6542 (tt) cc_final: 0.6293 (tp) REVERT: B 973 ASN cc_start: 0.7871 (m-40) cc_final: 0.7519 (m-40) REVERT: B 989 ARG cc_start: 0.7745 (ptm160) cc_final: 0.6647 (ttp-170) REVERT: C 85 MET cc_start: 0.1663 (tpt) cc_final: 0.0007 (ttm) REVERT: C 350 LEU cc_start: 0.8487 (mt) cc_final: 0.7759 (tp) REVERT: C 746 MET cc_start: 0.7562 (tmm) cc_final: 0.7225 (tmm) REVERT: C 773 GLN cc_start: 0.7603 (pp30) cc_final: 0.7179 (pp30) REVERT: C 1013 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7385 (mtm180) REVERT: C 1166 MET cc_start: 0.2060 (mmm) cc_final: 0.0026 (ptm) REVERT: C 1180 HIS cc_start: 0.4026 (t-90) cc_final: 0.2837 (p-80) REVERT: C 1235 ASP cc_start: 0.7343 (m-30) cc_final: 0.6677 (t70) REVERT: C 1294 LEU cc_start: 0.7994 (mt) cc_final: 0.7676 (mt) REVERT: C 1304 THR cc_start: 0.7758 (p) cc_final: 0.7452 (t) REVERT: C 1335 ARG cc_start: 0.7489 (tpm170) cc_final: 0.6871 (mtt90) REVERT: D 133 LEU cc_start: 0.7382 (mt) cc_final: 0.6936 (mt) REVERT: D 182 TYR cc_start: 0.6942 (t80) cc_final: 0.5909 (t80) REVERT: D 355 ASN cc_start: 0.8961 (t0) cc_final: 0.8714 (t0) REVERT: D 606 LEU cc_start: 0.6887 (mm) cc_final: 0.6679 (mm) REVERT: D 679 MET cc_start: 0.4458 (ppp) cc_final: 0.4168 (ppp) REVERT: D 835 MET cc_start: 0.7802 (mmm) cc_final: 0.7203 (mmt) REVERT: D 989 ARG cc_start: 0.7820 (ptm160) cc_final: 0.6724 (ttp-170) REVERT: D 1014 MET cc_start: 0.3392 (tpt) cc_final: 0.2816 (tpt) REVERT: D 1097 PHE cc_start: 0.6444 (t80) cc_final: 0.6241 (t80) REVERT: D 1104 LYS cc_start: 0.7759 (mmpt) cc_final: 0.7538 (tppt) REVERT: D 1105 MET cc_start: 0.6123 (mtt) cc_final: 0.5653 (mtt) outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.4883 time to fit residues: 482.4328 Evaluate side-chains 444 residues out of total 3948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 282 optimal weight: 0.2980 chunk 378 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 327 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 365 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 459 HIS A 519 HIS A 609 ASN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 672 ASN B 708 GLN B 727 GLN B 731 GLN C 183 GLN ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS C 519 HIS C 753 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** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.181419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.154239 restraints weight = 70980.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.153133 restraints weight = 83132.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.155053 restraints weight = 68131.036| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36046 Z= 0.162 Angle : 0.623 11.398 48820 Z= 0.314 Chirality : 0.045 0.227 5596 Planarity : 0.004 0.059 6294 Dihedral : 5.229 24.526 4816 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.85 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -3.04 (0.12), residues: 4454 helix: -1.07 (0.15), residues: 1102 sheet: -1.59 (0.16), residues: 990 loop : -2.74 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP C 135 HIS 0.005 0.001 HIS B 797 PHE 0.017 0.001 PHE A 464 TYR 0.017 0.001 TYR A 558 ARG 0.010 0.000 ARG B 111 =============================================================================== Job complete usr+sys time: 9277.26 seconds wall clock time: 168 minutes 44.63 seconds (10124.63 seconds total)