Starting phenix.real_space_refine on Tue Aug 26 16:31:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cq6_45809/08_2025/9cq6_45809.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cq6_45809/08_2025/9cq6_45809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cq6_45809/08_2025/9cq6_45809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cq6_45809/08_2025/9cq6_45809.map" model { file = "/net/cci-nas-00/data/ceres_data/9cq6_45809/08_2025/9cq6_45809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cq6_45809/08_2025/9cq6_45809.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 1.373 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: 5 Type Number sf(0) Gaussians P 148 5.49 5 S 200 5.16 5 C 24496 2.51 5 N 6672 2.21 5 O 7664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39180 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 4171 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 514, 4160 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 514, 4160 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain breaks: 1 bond proxies already assigned to first conformer: 4232 Chain: "B" Number of atoms: 4211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4211 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 26, 'TRANS': 499} Chain breaks: 1 Chain: "C" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1831 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "E" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "F" Number of atoms: 6865 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 853, 6854 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 37, 'TRANS': 815} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 853, 6854 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 37, 'TRANS': 815} Chain breaks: 2 bond proxies already assigned to first conformer: 6992 Chain: "G" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 174 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 3, 'TRANS': 20} Chain: "H" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 165 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 811 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 776 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 742 Classifications: {'DNA': 36} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 35} Chain: "L" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 700 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "a" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4094 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 28, 'TRANS': 478} Chain: "b" Number of atoms: 4223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4223 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 26, 'TRANS': 501} Chain breaks: 1 Chain: "c" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1813 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "d" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "e" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "f" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2069 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 10, 'TRANS': 244} Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 444 " occ=0.36 ... (20 atoms not shown) pdb=" NH2BARG A 444 " occ=0.64 residue: pdb=" N AARG F 603 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG F 603 " occ=0.40 Time building chain proxies: 11.29, per 1000 atoms: 0.29 Number of scatterers: 39180 At special positions: 0 Unit cell: (202.419, 241.57, 179.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 200 16.00 P 148 15.00 O 7664 8.00 N 6672 7.00 C 24496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 2.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8572 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 43 sheets defined 43.8% alpha, 19.5% beta 74 base pairs and 128 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 4.219A pdb=" N SER A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 58 through 78 removed outlier: 3.597A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.637A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 236 through 244 removed outlier: 4.341A pdb=" N GLU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.977A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.939A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 510 through 518 removed outlier: 3.630A pdb=" N MET A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.629A pdb=" N SER B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 87 through 97 removed outlier: 3.755A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 371 through 388 Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.632A pdb=" N LEU B 430 " --> pdb=" O MET B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.082A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.504A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 3.726A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing helix chain 'C' and resid 0 through 11 Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 68 through 86 Proline residue: C 82 - end of helix Processing helix chain 'C' and resid 127 through 170 removed outlier: 5.189A pdb=" N ARG C 137 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 197 through 202 Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 215 through 229 Processing helix chain 'D' and resid 49 through 60 removed outlier: 3.612A pdb=" N MET D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 75 Processing helix chain 'D' and resid 118 through 201 removed outlier: 3.765A pdb=" N VAL D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU D 199 " --> pdb=" O HIS D 195 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 62 through 75 Processing helix chain 'E' and resid 118 through 201 removed outlier: 4.568A pdb=" N VAL E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU E 170 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA E 201 " --> pdb=" O LYS E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 14 Processing helix chain 'F' and resid 15 through 29 removed outlier: 3.915A pdb=" N LEU F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 54 removed outlier: 3.639A pdb=" N LYS F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.973A pdb=" N LEU F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 76 Processing helix chain 'F' and resid 85 through 98 Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 114 through 118 removed outlier: 4.312A pdb=" N GLY F 117 " --> pdb=" O THR F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 134 Processing helix chain 'F' and resid 144 through 162 Processing helix chain 'F' and resid 163 through 177 removed outlier: 3.524A pdb=" N ILE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 192 Processing helix chain 'F' and resid 199 through 208 Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'F' and resid 220 through 228 Processing helix chain 'F' and resid 258 through 264 Processing helix chain 'F' and resid 298 through 303 Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 381 through 391 Processing helix chain 'F' and resid 410 through 424 removed outlier: 3.524A pdb=" N VAL F 414 " --> pdb=" O THR F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 477 removed outlier: 4.037A pdb=" N ARG F 476 " --> pdb=" O LYS F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 524 removed outlier: 4.577A pdb=" N LYS F 524 " --> pdb=" O LEU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 593 removed outlier: 4.002A pdb=" N CYS F 593 " --> pdb=" O TRP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 595 through 607 removed outlier: 4.143A pdb=" N ALA F 606 " --> pdb=" O LEU F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 685 removed outlier: 3.615A pdb=" N PHE F 685 " --> pdb=" O ARG F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 716 removed outlier: 3.749A pdb=" N ASN F 716 " --> pdb=" O ILE F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 722 through 732 removed outlier: 4.124A pdb=" N LEU F 726 " --> pdb=" O LYS F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 756 removed outlier: 4.179A pdb=" N ARG F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 781 removed outlier: 3.550A pdb=" N ILE F 781 " --> pdb=" O VAL F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 788 through 804 Processing helix chain 'F' and resid 805 through 808 removed outlier: 3.704A pdb=" N SER F 808 " --> pdb=" O TRP F 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 805 through 808' Processing helix chain 'F' and resid 836 through 849 removed outlier: 4.067A pdb=" N ILE F 840 " --> pdb=" O THR F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 882 Processing helix chain 'F' and resid 891 through 901 removed outlier: 3.739A pdb=" N THR F 895 " --> pdb=" O GLU F 891 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP F 899 " --> pdb=" O THR F 895 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS F 900 " --> pdb=" O ASP F 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 905 through 909 removed outlier: 3.904A pdb=" N GLN F 908 " --> pdb=" O GLU F 905 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 50 Processing helix chain 'a' and resid 58 through 78 Processing helix chain 'a' and resid 112 through 121 Processing helix chain 'a' and resid 124 through 135 Processing helix chain 'a' and resid 142 through 157 removed outlier: 3.502A pdb=" N VAL a 157 " --> pdb=" O LEU a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 197 removed outlier: 3.911A pdb=" N ALA a 183 " --> pdb=" O ASP a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 220 removed outlier: 3.951A pdb=" N ASP a 219 " --> pdb=" O PHE a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 244 removed outlier: 3.741A pdb=" N ASP a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 330 through 338 removed outlier: 3.850A pdb=" N LYS a 338 " --> pdb=" O THR a 334 " (cutoff:3.500A) Processing helix chain 'a' and resid 354 through 356 No H-bonds generated for 'chain 'a' and resid 354 through 356' Processing helix chain 'a' and resid 377 through 393 removed outlier: 3.796A pdb=" N LEU a 381 " --> pdb=" O GLY a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 469 Processing helix chain 'a' and resid 480 through 496 Processing helix chain 'a' and resid 510 through 519 removed outlier: 3.699A pdb=" N MET a 514 " --> pdb=" O LYS a 510 " (cutoff:3.500A) Processing helix chain 'a' and resid 520 through 530 Processing helix chain 'b' and resid 17 through 22 removed outlier: 3.665A pdb=" N SER b 21 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 48 Processing helix chain 'b' and resid 87 through 96 removed outlier: 3.733A pdb=" N LEU b 91 " --> pdb=" O ASP b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 122 Processing helix chain 'b' and resid 146 through 158 Processing helix chain 'b' and resid 198 through 216 removed outlier: 3.801A pdb=" N GLU b 206 " --> pdb=" O LYS b 202 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE b 207 " --> pdb=" O GLU b 203 " (cutoff:3.500A) Processing helix chain 'b' and resid 217 through 222 Processing helix chain 'b' and resid 227 through 231 Processing helix chain 'b' and resid 324 through 332 Processing helix chain 'b' and resid 349 through 351 No H-bonds generated for 'chain 'b' and resid 349 through 351' Processing helix chain 'b' and resid 352 through 356 Processing helix chain 'b' and resid 370 through 388 removed outlier: 3.598A pdb=" N ALA b 374 " --> pdb=" O ASP b 370 " (cutoff:3.500A) Processing helix chain 'b' and resid 426 through 430 Processing helix chain 'b' and resid 447 through 461 Processing helix chain 'b' and resid 478 through 482 Processing helix chain 'b' and resid 484 through 500 removed outlier: 3.965A pdb=" N GLN b 488 " --> pdb=" O ASN b 484 " (cutoff:3.500A) Processing helix chain 'b' and resid 509 through 517 Processing helix chain 'b' and resid 519 through 526 removed outlier: 3.568A pdb=" N THR b 523 " --> pdb=" O PRO b 519 " (cutoff:3.500A) Processing helix chain 'b' and resid 526 through 537 Processing helix chain 'c' and resid 1 through 10 Processing helix chain 'c' and resid 51 through 62 Processing helix chain 'c' and resid 68 through 86 Proline residue: c 82 - end of helix Processing helix chain 'c' and resid 127 through 170 removed outlier: 5.060A pdb=" N ARG c 137 " --> pdb=" O GLN c 133 " (cutoff:3.500A) Proline residue: c 138 - end of helix removed outlier: 3.554A pdb=" N SER c 170 " --> pdb=" O ASP c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 176 through 180 removed outlier: 3.945A pdb=" N LEU c 179 " --> pdb=" O ARG c 176 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS c 180 " --> pdb=" O ASP c 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 176 through 180' Processing helix chain 'c' and resid 185 through 197 Processing helix chain 'c' and resid 197 through 202 Processing helix chain 'c' and resid 207 through 214 removed outlier: 3.667A pdb=" N LEU c 214 " --> pdb=" O PHE c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 214 through 227 Processing helix chain 'd' and resid 27 through 31 removed outlier: 3.648A pdb=" N SER d 30 " --> pdb=" O THR d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 60 Processing helix chain 'd' and resid 62 through 75 Processing helix chain 'd' and resid 119 through 201 Processing helix chain 'e' and resid 49 through 60 Processing helix chain 'e' and resid 62 through 75 Processing helix chain 'e' and resid 118 through 201 removed outlier: 3.804A pdb=" N VAL e 122 " --> pdb=" O ASN e 118 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU e 170 " --> pdb=" O VAL e 166 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA e 171 " --> pdb=" O SER e 167 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU e 173 " --> pdb=" O LYS e 169 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR e 174 " --> pdb=" O GLU e 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 674 through 685 Processing helix chain 'f' and resid 706 through 715 Processing helix chain 'f' and resid 723 through 733 Processing helix chain 'f' and resid 747 through 758 removed outlier: 3.693A pdb=" N ARG f 756 " --> pdb=" O GLU f 752 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU f 757 " --> pdb=" O HIS f 753 " (cutoff:3.500A) Processing helix chain 'f' and resid 770 through 781 removed outlier: 3.666A pdb=" N ILE f 781 " --> pdb=" O VAL f 777 " (cutoff:3.500A) Processing helix chain 'f' and resid 788 through 804 Processing helix chain 'f' and resid 836 through 849 removed outlier: 4.200A pdb=" N ILE f 840 " --> pdb=" O THR f 836 " (cutoff:3.500A) Processing helix chain 'f' and resid 871 through 882 Processing helix chain 'f' and resid 891 through 901 removed outlier: 3.508A pdb=" N THR f 895 " --> pdb=" O GLU f 891 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP f 899 " --> pdb=" O THR f 895 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS f 900 " --> pdb=" O ASP f 896 " (cutoff:3.500A) Processing helix chain 'f' and resid 905 through 909 removed outlier: 3.773A pdb=" N GLN f 908 " --> pdb=" O GLU f 905 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 6.480A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU A 107 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU A 83 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG A 35 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ARG A 165 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER A 37 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N MET A 167 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 39 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE A 169 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 41 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 168 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.625A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 431 " --> pdb=" O GLN A 416 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA A 395 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE A 350 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 397 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 345 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 304 removed outlier: 4.464A pdb=" N TYR B 295 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.688A pdb=" N ILE B 540 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.802A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.283A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA B 8 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA B 55 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 10 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL B 57 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU B 12 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE B 59 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N MET B 14 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 9 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLU B 133 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL B 11 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE B 135 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N CYS B 13 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N TYR B 225 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.753A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU B 268 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N ASN B 359 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE B 340 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 464 through 466 Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 18 removed outlier: 3.600A pdb=" N ASN C 21 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN C 48 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N HIS C 122 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 10.507A pdb=" N ASP C 50 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 11.802A pdb=" N ASN C 120 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 100 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.129A pdb=" N ARG E 107 " --> pdb=" O LYS E 99 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS E 99 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL E 83 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 9 Processing sheet with id=AB6, first strand: chain 'D' and resid 85 through 89 removed outlier: 4.139A pdb=" N PHE D 97 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY D 109 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 2 through 9 Processing sheet with id=AB8, first strand: chain 'F' and resid 250 through 253 removed outlier: 7.092A pdb=" N LEU F 250 " --> pdb=" O TRP F 447 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LYS F 449 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA F 252 " --> pdb=" O LYS F 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 287 through 291 removed outlier: 6.985A pdb=" N ILE F 325 " --> pdb=" O MET F 371 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET F 371 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE F 327 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL F 369 " --> pdb=" O ILE F 327 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP F 329 " --> pdb=" O PHE F 367 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 341 through 343 removed outlier: 4.249A pdb=" N ALA F 334 " --> pdb=" O MET F 343 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE F 325 " --> pdb=" O MET F 371 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET F 371 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE F 327 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL F 369 " --> pdb=" O ILE F 327 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP F 329 " --> pdb=" O PHE F 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 527 through 528 removed outlier: 10.310A pdb=" N ILE F 464 " --> pdb=" O ALA F 488 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ALA F 488 " --> pdb=" O ILE F 464 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE F 466 " --> pdb=" O ALA F 486 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA F 486 " --> pdb=" O ILE F 466 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS F 482 " --> pdb=" O TYR F 470 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER F 504 " --> pdb=" O CYS F 485 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL F 487 " --> pdb=" O THR F 502 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N THR F 502 " --> pdb=" O VAL F 487 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE F 500 " --> pdb=" O LEU F 539 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 527 through 528 removed outlier: 6.061A pdb=" N ILE F 556 " --> pdb=" O ILE F 584 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE F 584 " --> pdb=" O ILE F 556 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN F 558 " --> pdb=" O GLU F 582 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 563 through 566 removed outlier: 4.020A pdb=" N GLU F 563 " --> pdb=" O ARG F 577 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 688 through 689 removed outlier: 7.307A pdb=" N GLU F 663 " --> pdb=" O CYS F 699 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE F 701 " --> pdb=" O GLU F 663 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS F 665 " --> pdb=" O ILE F 701 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL F 700 " --> pdb=" O VAL F 721 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 851 through 852 removed outlier: 6.238A pdb=" N THR F 817 " --> pdb=" O HIS F 862 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE F 864 " --> pdb=" O THR F 817 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR F 819 " --> pdb=" O ILE F 864 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL F 863 " --> pdb=" O LEU F 889 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 102 through 109 removed outlier: 6.498A pdb=" N VAL a 85 " --> pdb=" O LEU a 105 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLU a 107 " --> pdb=" O LEU a 83 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU a 83 " --> pdb=" O GLU a 107 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP a 36 " --> pdb=" O LEU a 82 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ALA a 84 " --> pdb=" O ASP a 36 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU a 38 " --> pdb=" O ALA a 84 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL a 86 " --> pdb=" O LEU a 38 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE a 40 " --> pdb=" O VAL a 86 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR a 88 " --> pdb=" O PHE a 40 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL a 42 " --> pdb=" O TYR a 88 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG a 35 " --> pdb=" O HIS a 163 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ARG a 165 " --> pdb=" O ARG a 35 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER a 37 " --> pdb=" O ARG a 165 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N MET a 167 " --> pdb=" O SER a 37 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE a 39 " --> pdb=" O MET a 167 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE a 169 " --> pdb=" O ILE a 39 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU a 41 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N PHE a 199 " --> pdb=" O SER a 162 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS a 164 " --> pdb=" O PHE a 199 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASP a 201 " --> pdb=" O LYS a 164 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE a 166 " --> pdb=" O ASP a 201 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'a' and resid 211 through 212 Processing sheet with id=AC9, first strand: chain 'a' and resid 257 through 262 removed outlier: 3.526A pdb=" N SER a 257 " --> pdb=" O ILE a 273 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL a 394 " --> pdb=" O PRO a 415 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA a 395 " --> pdb=" O PHE a 350 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE a 350 " --> pdb=" O ALA a 395 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU a 397 " --> pdb=" O MET a 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 286 through 289 Processing sheet with id=AD2, first strand: chain 'a' and resid 296 through 304 removed outlier: 4.333A pdb=" N TYR b 295 " --> pdb=" O VAL b 305 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'a' and resid 325 through 329 Processing sheet with id=AD4, first strand: chain 'a' and resid 375 through 376 Processing sheet with id=AD5, first strand: chain 'a' and resid 419 through 421 removed outlier: 6.543A pdb=" N GLU a 419 " --> pdb=" O VAL a 427 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE a 425 " --> pdb=" O ASP a 421 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'b' and resid 77 through 84 removed outlier: 6.496A pdb=" N LEU b 56 " --> pdb=" O HIS b 80 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N HIS b 82 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE b 54 " --> pdb=" O HIS b 82 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL b 10 " --> pdb=" O ALA b 55 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL b 57 " --> pdb=" O VAL b 10 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU b 12 " --> pdb=" O VAL b 57 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE b 59 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N MET b 14 " --> pdb=" O PHE b 59 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG b 130 " --> pdb=" O SER b 160 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLN b 162 " --> pdb=" O ARG b 130 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE b 132 " --> pdb=" O GLN b 162 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE b 164 " --> pdb=" O ILE b 132 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE b 134 " --> pdb=" O PHE b 164 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N TYR b 225 " --> pdb=" O LEU b 161 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE b 163 " --> pdb=" O TYR b 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 247 through 252 removed outlier: 6.830A pdb=" N VAL b 361 " --> pdb=" O SER b 266 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU b 268 " --> pdb=" O ASN b 359 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N ASN b 359 " --> pdb=" O LEU b 268 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N GLN b 360 " --> pdb=" O GLN b 423 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN b 423 " --> pdb=" O GLN b 360 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA b 366 " --> pdb=" O GLU b 417 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N GLU b 417 " --> pdb=" O ALA b 366 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N MET b 389 " --> pdb=" O PRO b 410 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL b 390 " --> pdb=" O PHE b 345 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE b 345 " --> pdb=" O VAL b 390 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE b 392 " --> pdb=" O LEU b 343 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS b 339 " --> pdb=" O ALA b 396 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE b 340 " --> pdb=" O PRO b 248 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG b 250 " --> pdb=" O PHE b 340 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL b 342 " --> pdb=" O ARG b 250 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N THR b 252 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLY b 344 " --> pdb=" O THR b 252 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'b' and resid 464 through 467 Processing sheet with id=AD9, first strand: chain 'c' and resid 14 through 17 removed outlier: 6.705A pdb=" N GLN c 48 " --> pdb=" O HIS c 122 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N HIS c 122 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N ASP c 50 " --> pdb=" O ASN c 120 " (cutoff:3.500A) removed outlier: 12.163A pdb=" N ASN c 120 " --> pdb=" O ASP c 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 65 through 66 removed outlier: 6.756A pdb=" N PHE e 97 " --> pdb=" O LEU e 108 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER e 110 " --> pdb=" O PHE e 95 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE e 95 " --> pdb=" O SER e 110 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL e 83 " --> pdb=" O ASN e 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 2 through 8 Processing sheet with id=AE3, first strand: chain 'd' and resid 83 through 89 removed outlier: 4.296A pdb=" N VAL d 83 " --> pdb=" O ASN d 100 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS d 99 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG d 107 " --> pdb=" O LYS d 99 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU d 101 " --> pdb=" O SER d 105 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER d 105 " --> pdb=" O LEU d 101 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'e' and resid 2 through 8 Processing sheet with id=AE5, first strand: chain 'f' and resid 664 through 666 removed outlier: 6.230A pdb=" N CYS f 665 " --> pdb=" O ILE f 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'f' and resid 720 through 721 removed outlier: 6.771A pdb=" N VAL f 720 " --> pdb=" O ILE f 744 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'f' and resid 851 through 852 removed outlier: 6.092A pdb=" N THR f 817 " --> pdb=" O HIS f 862 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE f 864 " --> pdb=" O THR f 817 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR f 819 " --> pdb=" O ILE f 864 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL f 863 " --> pdb=" O LEU f 889 " (cutoff:3.500A) 1819 hydrogen bonds defined for protein. 5161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 179 hydrogen bonds 358 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 128 stacking parallelities Total time for adding SS restraints: 11.00 Time building geometry restraints manager: 4.42 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: 12175 1.34 - 1.46: 7038 1.46 - 1.58: 20466 1.58 - 1.70: 292 1.70 - 1.82: 316 Bond restraints: 40287 Sorted by residual: bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N MET e 1 " pdb=" CA MET e 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N MET d 1 " pdb=" CA MET d 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N VAL c 0 " pdb=" CA VAL c 0 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 ... (remaining 40282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 54384 1.97 - 3.93: 576 3.93 - 5.90: 25 5.90 - 7.86: 3 7.86 - 9.83: 3 Bond angle restraints: 54991 Sorted by residual: angle pdb=" C1' AMP L1001 " pdb=" C2' AMP L1001 " pdb=" C3' AMP L1001 " ideal model delta sigma weight residual 111.00 101.17 9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CB MET E 1 " pdb=" CG MET E 1 " pdb=" SD MET E 1 " ideal model delta sigma weight residual 112.70 122.07 -9.37 3.00e+00 1.11e-01 9.76e+00 angle pdb=" OG1 THR A 10 " pdb=" CB THR A 10 " pdb=" CG2 THR A 10 " ideal model delta sigma weight residual 109.30 103.34 5.96 2.00e+00 2.50e-01 8.87e+00 angle pdb=" C ASN a 515 " pdb=" CA ASN a 515 " pdb=" CB ASN a 515 " ideal model delta sigma weight residual 110.88 106.21 4.67 1.57e+00 4.06e-01 8.87e+00 angle pdb=" C2' AMP L1001 " pdb=" C3' AMP L1001 " pdb=" C4' AMP L1001 " ideal model delta sigma weight residual 111.00 102.40 8.60 3.00e+00 1.11e-01 8.22e+00 ... (remaining 54986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 20139 17.98 - 35.96: 2772 35.96 - 53.94: 1023 53.94 - 71.92: 248 71.92 - 89.90: 57 Dihedral angle restraints: 24239 sinusoidal: 11062 harmonic: 13177 Sorted by residual: dihedral pdb=" C4' AMP L1001 " pdb=" C5' AMP L1001 " pdb=" O5' AMP L1001 " pdb=" P AMP L1001 " ideal model delta sinusoidal sigma weight residual 180.00 93.52 86.48 1 2.00e+01 2.50e-03 2.25e+01 dihedral pdb=" C2' AMP L1001 " pdb=" C1' AMP L1001 " pdb=" N9 AMP L1001 " pdb=" C4 AMP L1001 " ideal model delta sinusoidal sigma weight residual 91.55 24.90 66.65 1 2.00e+01 2.50e-03 1.45e+01 dihedral pdb=" CA ASP D 57 " pdb=" CB ASP D 57 " pdb=" CG ASP D 57 " pdb=" OD1 ASP D 57 " ideal model delta sinusoidal sigma weight residual -30.00 -88.65 58.65 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 24236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4964 0.041 - 0.083: 745 0.083 - 0.124: 360 0.124 - 0.165: 32 0.165 - 0.207: 1 Chirality restraints: 6102 Sorted by residual: chirality pdb=" C3' AMP L1001 " pdb=" C2' AMP L1001 " pdb=" C4' AMP L1001 " pdb=" O3' AMP L1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR A 10 " pdb=" CA THR A 10 " pdb=" OG1 THR A 10 " pdb=" CG2 THR A 10 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA ILE F 325 " pdb=" N ILE F 325 " pdb=" C ILE F 325 " pdb=" CB ILE F 325 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 6099 not shown) Planarity restraints: 6544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP e 103 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" CG ASP e 103 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP e 103 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP e 103 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 185 " 0.181 9.50e-02 1.11e+02 8.15e-02 4.72e+00 pdb=" NE ARG A 185 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 185 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 185 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 185 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 455 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A 456 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " -0.028 5.00e-02 4.00e+02 ... (remaining 6541 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5711 2.76 - 3.29: 37060 3.29 - 3.83: 66397 3.83 - 4.36: 74704 4.36 - 4.90: 128522 Nonbonded interactions: 312394 Sorted by model distance: nonbonded pdb=" NZ LYS F 164 " pdb=" OP1 DA K 5 " model vdw 2.224 3.120 nonbonded pdb=" OE1 GLU A 372 " pdb=" OH TYR B 444 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR f 819 " pdb=" O SER f 854 " model vdw 2.317 3.040 nonbonded pdb=" N GLU c 182 " pdb=" OE1 GLU c 182 " model vdw 2.319 3.120 nonbonded pdb=" O SER B 69 " pdb=" OG SER B 69 " model vdw 2.343 3.040 ... (remaining 312389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 443 or resid 445 through 536)) selection = (chain 'a' and (resid 32 through 443 or resid 445 through 536)) } ncs_group { reference = chain 'B' selection = (chain 'b' and (resid 6 through 169 or resid 181 through 542)) } ncs_group { reference = (chain 'C' and resid 0 through 227) selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'd' selection = chain 'e' } ncs_group { reference = (chain 'G' and resid 180 through 202) selection = chain 'H' } 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=0.36 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 12.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.920 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 46.280 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.002 0.092 40288 Z= 0.105 Angle : 0.457 9.827 54991 Z= 0.243 Chirality : 0.038 0.207 6102 Planarity : 0.003 0.082 6544 Dihedral : 19.158 89.901 15667 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.12 % Allowed : 19.92 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.13), residues: 4461 helix: 3.63 (0.13), residues: 1749 sheet: 0.74 (0.19), residues: 758 loop : 0.14 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 185 TYR 0.008 0.001 TYR c 34 PHE 0.027 0.001 PHE F 730 TRP 0.006 0.000 TRP F 893 HIS 0.003 0.000 HIS F 482 Details of bonding type rmsd covalent geometry : bond 0.00207 (40287) covalent geometry : angle 0.45725 (54991) hydrogen bonds : bond 0.10888 ( 1987) hydrogen bonds : angle 4.96402 ( 5519) Misc. bond : bond 0.09174 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 478 time to evaluate : 1.737 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: B 154 LEU cc_start: 0.9509 (mt) cc_final: 0.9191 (mp) REVERT: D 37 THR cc_start: 0.8914 (m) cc_final: 0.8678 (p) REVERT: D 129 TYR cc_start: 0.7618 (t80) cc_final: 0.7359 (t80) REVERT: D 192 ARG cc_start: 0.8685 (mpt180) cc_final: 0.8364 (mmm160) REVERT: F 44 ASP cc_start: 0.8073 (t70) cc_final: 0.7859 (t70) REVERT: a 409 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.7709 (t80) REVERT: b 18 PHE cc_start: 0.7677 (t80) cc_final: 0.7410 (t80) REVERT: e 174 THR cc_start: 0.9192 (m) cc_final: 0.8978 (p) REVERT: f 909 TYR cc_start: 0.5901 (m-80) cc_final: 0.4801 (m-80) outliers start: 5 outliers final: 0 residues processed: 482 average time/residue: 0.2794 time to fit residues: 213.8823 Evaluate side-chains 330 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 409 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 132 GLN A 137 HIS B 22 ASN B 243 HIS E 40 HIS F 119 HIS F 183 GLN a 137 HIS a 515 ASN b 76 ASN ** b 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 256 ASN b 488 GLN d 9 HIS d 21 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.080659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052572 restraints weight = 240054.777| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 5.35 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40288 Z= 0.189 Angle : 0.584 9.152 54991 Z= 0.303 Chirality : 0.040 0.295 6102 Planarity : 0.004 0.056 6544 Dihedral : 16.465 77.349 6467 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.94 % Allowed : 20.74 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.13), residues: 4461 helix: 3.04 (0.12), residues: 1781 sheet: 0.73 (0.19), residues: 756 loop : 0.00 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 218 TYR 0.022 0.001 TYR f 909 PHE 0.028 0.001 PHE A 216 TRP 0.039 0.002 TRP F 738 HIS 0.007 0.001 HIS F 215 Details of bonding type rmsd covalent geometry : bond 0.00434 (40287) covalent geometry : angle 0.58350 (54991) hydrogen bonds : bond 0.03591 ( 1987) hydrogen bonds : angle 4.40534 ( 5519) Misc. bond : bond 0.00325 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 340 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7199 (t80) REVERT: B 288 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8315 (t0) REVERT: C 156 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8765 (tt) REVERT: D 10 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8398 (tp) REVERT: D 37 THR cc_start: 0.9124 (m) cc_final: 0.8768 (p) REVERT: D 52 ILE cc_start: 0.8714 (tt) cc_final: 0.8499 (pt) REVERT: D 71 ARG cc_start: 0.9086 (mtp-110) cc_final: 0.8872 (mtt-85) REVERT: D 84 TYR cc_start: 0.7055 (m-80) cc_final: 0.5621 (m-80) REVERT: D 151 LEU cc_start: 0.9758 (OUTLIER) cc_final: 0.9497 (tp) REVERT: D 192 ARG cc_start: 0.9263 (mpt180) cc_final: 0.8660 (mmm160) REVERT: E 103 ASP cc_start: 0.8408 (t0) cc_final: 0.8057 (t0) REVERT: F 44 ASP cc_start: 0.9187 (t70) cc_final: 0.8912 (t70) REVERT: F 150 ASP cc_start: 0.9064 (m-30) cc_final: 0.8757 (t0) REVERT: F 333 MET cc_start: 0.7690 (mmm) cc_final: 0.7394 (mmm) REVERT: F 368 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8603 (m-30) REVERT: F 430 MET cc_start: 0.8889 (mtp) cc_final: 0.8635 (mtp) REVERT: F 751 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9167 (mtmm) REVERT: F 848 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.8477 (t70) REVERT: a 135 MET cc_start: 0.9244 (mtt) cc_final: 0.8859 (mtt) REVERT: a 142 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.7968 (p) REVERT: a 409 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7361 (t80) REVERT: b 210 MET cc_start: 0.9435 (ppp) cc_final: 0.9227 (ppp) REVERT: c 219 MET cc_start: 0.8437 (mtm) cc_final: 0.8131 (mtm) REVERT: d 24 TRP cc_start: 0.8139 (p-90) cc_final: 0.7907 (p-90) REVERT: d 54 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9099 (tm-30) REVERT: d 59 MET cc_start: 0.8198 (tpp) cc_final: 0.7552 (mtt) REVERT: d 72 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7765 (pttt) REVERT: d 157 ASP cc_start: 0.9627 (t0) cc_final: 0.9336 (t0) REVERT: e 57 ASP cc_start: 0.8775 (m-30) cc_final: 0.8552 (p0) REVERT: e 172 LEU cc_start: 0.9423 (mt) cc_final: 0.9069 (mt) REVERT: e 174 THR cc_start: 0.9591 (m) cc_final: 0.9363 (p) REVERT: e 182 LEU cc_start: 0.9614 (tt) cc_final: 0.9394 (pp) REVERT: f 698 TYR cc_start: 0.8614 (t80) cc_final: 0.8329 (t80) REVERT: f 773 GLN cc_start: 0.9413 (mp10) cc_final: 0.9011 (mp10) outliers start: 78 outliers final: 28 residues processed: 399 average time/residue: 0.2577 time to fit residues: 168.2376 Evaluate side-chains 350 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 312 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 730 PHE Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 128 CYS Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 848 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 191 optimal weight: 0.9990 chunk 270 optimal weight: 0.9990 chunk 363 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 304 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 414 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 319 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN B 45 GLN B 496 HIS C 215 GLN E 40 HIS F 119 HIS ** F 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 360 HIS b 22 ASN ** b 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS c 147 GLN d 18 HIS d 21 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.079434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.051046 restraints weight = 251643.978| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 5.46 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 40288 Z= 0.202 Angle : 0.565 8.647 54991 Z= 0.293 Chirality : 0.040 0.194 6102 Planarity : 0.004 0.060 6544 Dihedral : 16.682 77.726 6467 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.03 % Allowed : 20.64 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.13), residues: 4461 helix: 2.84 (0.12), residues: 1781 sheet: 0.69 (0.19), residues: 770 loop : -0.14 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG d 161 TYR 0.017 0.001 TYR f 801 PHE 0.030 0.001 PHE B 107 TRP 0.040 0.001 TRP F 805 HIS 0.007 0.001 HIS F 282 Details of bonding type rmsd covalent geometry : bond 0.00462 (40287) covalent geometry : angle 0.56516 (54991) hydrogen bonds : bond 0.03476 ( 1987) hydrogen bonds : angle 4.32740 ( 5519) Misc. bond : bond 0.00113 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 316 time to evaluate : 1.465 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: A 409 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.6863 (t80) REVERT: B 288 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8326 (t0) REVERT: C 104 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8277 (tt) REVERT: C 156 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8756 (tt) REVERT: D 37 THR cc_start: 0.9082 (m) cc_final: 0.8796 (p) REVERT: D 52 ILE cc_start: 0.8755 (tt) cc_final: 0.8529 (pt) REVERT: D 132 ASP cc_start: 0.9270 (m-30) cc_final: 0.8995 (p0) REVERT: D 151 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9564 (tp) REVERT: D 192 ARG cc_start: 0.9293 (mpt180) cc_final: 0.8667 (mmm160) REVERT: E 103 ASP cc_start: 0.8663 (t0) cc_final: 0.8254 (t0) REVERT: F 44 ASP cc_start: 0.9235 (t70) cc_final: 0.8916 (t70) REVERT: F 95 GLU cc_start: 0.8844 (tt0) cc_final: 0.8624 (tt0) REVERT: F 263 MET cc_start: 0.8310 (mmp) cc_final: 0.7828 (mmm) REVERT: F 279 MET cc_start: 0.8328 (mmm) cc_final: 0.7979 (mmm) REVERT: F 746 MET cc_start: 0.7976 (ttm) cc_final: 0.7476 (ttt) REVERT: F 848 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.8468 (t-90) REVERT: a 134 MET cc_start: 0.9168 (tmm) cc_final: 0.8840 (tmm) REVERT: a 135 MET cc_start: 0.9172 (mtt) cc_final: 0.8535 (mtt) REVERT: a 142 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7936 (p) REVERT: a 252 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7683 (mtm180) REVERT: c 219 MET cc_start: 0.8489 (mtm) cc_final: 0.8164 (mtm) REVERT: d 24 TRP cc_start: 0.8384 (p-90) cc_final: 0.8084 (p-90) REVERT: d 46 THR cc_start: 0.8860 (p) cc_final: 0.8539 (t) REVERT: d 161 ARG cc_start: 0.9018 (ttp-110) cc_final: 0.8672 (ttp-110) REVERT: e 20 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8769 (pt) REVERT: e 57 ASP cc_start: 0.8858 (m-30) cc_final: 0.8607 (p0) REVERT: e 172 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9062 (mt) REVERT: e 174 THR cc_start: 0.9617 (m) cc_final: 0.9394 (p) REVERT: f 746 MET cc_start: 0.8014 (mmp) cc_final: 0.7552 (mmm) REVERT: f 773 GLN cc_start: 0.9369 (mp10) cc_final: 0.9131 (mp10) outliers start: 82 outliers final: 47 residues processed: 383 average time/residue: 0.2620 time to fit residues: 163.4146 Evaluate side-chains 356 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 730 PHE Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 360 HIS Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 188 SER Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 108 LEU Chi-restraints excluded: chain e residue 172 LEU Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 712 ILE Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 776 GLU Chi-restraints excluded: chain f residue 820 LEU Chi-restraints excluded: chain f residue 848 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 391 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 227 optimal weight: 0.2980 chunk 370 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 368 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 435 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 360 HIS C 215 GLN F 119 HIS ** F 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 95 ASN a 360 HIS ** b 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 21 GLN e 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.080341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.051903 restraints weight = 239977.312| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 5.42 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 40288 Z= 0.119 Angle : 0.532 9.715 54991 Z= 0.276 Chirality : 0.039 0.217 6102 Planarity : 0.003 0.059 6544 Dihedral : 16.664 77.471 6467 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.91 % Allowed : 21.19 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.13), residues: 4461 helix: 2.84 (0.13), residues: 1780 sheet: 0.71 (0.19), residues: 769 loop : -0.18 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 153 TYR 0.018 0.001 TYR f 801 PHE 0.030 0.001 PHE B 107 TRP 0.024 0.001 TRP F 805 HIS 0.008 0.001 HIS a 360 Details of bonding type rmsd covalent geometry : bond 0.00264 (40287) covalent geometry : angle 0.53211 (54991) hydrogen bonds : bond 0.03203 ( 1987) hydrogen bonds : angle 4.20043 ( 5519) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 315 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.6884 (t80) REVERT: B 20 MET cc_start: 0.7935 (tpp) cc_final: 0.7316 (tpp) REVERT: B 288 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8346 (t0) REVERT: C 98 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8546 (m-30) REVERT: C 104 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8328 (tt) REVERT: C 156 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8823 (tt) REVERT: D 10 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8403 (tp) REVERT: D 52 ILE cc_start: 0.8740 (tt) cc_final: 0.8517 (pt) REVERT: D 132 ASP cc_start: 0.9195 (m-30) cc_final: 0.8915 (p0) REVERT: D 192 ARG cc_start: 0.9270 (mpt180) cc_final: 0.8637 (mmm160) REVERT: E 103 ASP cc_start: 0.8648 (t0) cc_final: 0.8195 (t0) REVERT: F 44 ASP cc_start: 0.9160 (t70) cc_final: 0.8840 (t70) REVERT: F 95 GLU cc_start: 0.8830 (tt0) cc_final: 0.8583 (tt0) REVERT: F 263 MET cc_start: 0.8264 (mmp) cc_final: 0.7775 (mmm) REVERT: F 279 MET cc_start: 0.8117 (mmm) cc_final: 0.7707 (mmm) REVERT: F 430 MET cc_start: 0.8942 (mtp) cc_final: 0.8681 (mtp) REVERT: F 569 MET cc_start: 0.9253 (mtp) cc_final: 0.8508 (mmm) REVERT: F 743 MET cc_start: 0.8845 (mmt) cc_final: 0.8548 (mmm) REVERT: F 746 MET cc_start: 0.7989 (ttm) cc_final: 0.7462 (ttt) REVERT: F 848 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8464 (t-90) REVERT: a 134 MET cc_start: 0.9252 (tmm) cc_final: 0.8936 (tmm) REVERT: a 142 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7981 (p) REVERT: a 252 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7788 (mtp85) REVERT: a 379 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8851 (m) REVERT: a 409 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7317 (t80) REVERT: c 219 MET cc_start: 0.8461 (mtm) cc_final: 0.8120 (mtm) REVERT: d 24 TRP cc_start: 0.8464 (p-90) cc_final: 0.8140 (p-90) REVERT: d 46 THR cc_start: 0.8881 (p) cc_final: 0.8587 (t) REVERT: d 54 GLN cc_start: 0.9378 (tm-30) cc_final: 0.9127 (tm-30) REVERT: d 59 MET cc_start: 0.8128 (tpp) cc_final: 0.7522 (mtt) REVERT: d 161 ARG cc_start: 0.8968 (ttp-110) cc_final: 0.8689 (ttp-110) REVERT: e 20 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8800 (pt) REVERT: e 57 ASP cc_start: 0.8847 (m-30) cc_final: 0.8570 (p0) REVERT: e 172 LEU cc_start: 0.9407 (mt) cc_final: 0.9050 (mt) REVERT: e 174 THR cc_start: 0.9600 (m) cc_final: 0.9369 (p) REVERT: f 746 MET cc_start: 0.7809 (mmp) cc_final: 0.7332 (mmm) REVERT: f 773 GLN cc_start: 0.9391 (mp10) cc_final: 0.9123 (mp10) REVERT: f 823 TYR cc_start: 0.7545 (m-80) cc_final: 0.7313 (m-80) outliers start: 77 outliers final: 38 residues processed: 379 average time/residue: 0.2551 time to fit residues: 158.2709 Evaluate side-chains 352 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 730 PHE Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 281 LEU Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 379 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain c residue 64 ARG Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 108 LEU Chi-restraints excluded: chain e residue 128 CYS Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 776 GLU Chi-restraints excluded: chain f residue 820 LEU Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 895 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 255 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 442 optimal weight: 9.9990 chunk 351 optimal weight: 0.5980 chunk 454 optimal weight: 20.0000 chunk 391 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 421 optimal weight: 1.9990 chunk 423 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN B 243 HIS F 119 HIS ** F 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 360 HIS ** b 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.079022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050480 restraints weight = 228209.715| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 5.27 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40288 Z= 0.191 Angle : 0.551 8.915 54991 Z= 0.285 Chirality : 0.039 0.216 6102 Planarity : 0.003 0.060 6544 Dihedral : 16.769 76.829 6467 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.26 % Allowed : 20.99 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.13), residues: 4461 helix: 2.76 (0.13), residues: 1786 sheet: 0.64 (0.19), residues: 766 loop : -0.19 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 150 TYR 0.022 0.001 TYR f 698 PHE 0.027 0.001 PHE B 107 TRP 0.038 0.001 TRP F 738 HIS 0.006 0.001 HIS F 282 Details of bonding type rmsd covalent geometry : bond 0.00439 (40287) covalent geometry : angle 0.55084 (54991) hydrogen bonds : bond 0.03378 ( 1987) hydrogen bonds : angle 4.23520 ( 5519) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 302 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7726 (ttt-90) REVERT: A 409 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.6802 (t80) REVERT: B 20 MET cc_start: 0.7968 (tpp) cc_final: 0.7319 (tpp) REVERT: B 288 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8331 (t0) REVERT: C 98 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8473 (m-30) REVERT: D 10 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8456 (tp) REVERT: D 52 ILE cc_start: 0.8743 (tt) cc_final: 0.8512 (pt) REVERT: D 71 ARG cc_start: 0.9119 (mtp-110) cc_final: 0.8801 (mtt-85) REVERT: D 151 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9561 (tp) REVERT: E 103 ASP cc_start: 0.8792 (t0) cc_final: 0.8349 (t0) REVERT: F 44 ASP cc_start: 0.9248 (t70) cc_final: 0.8938 (t70) REVERT: F 95 GLU cc_start: 0.8846 (tt0) cc_final: 0.8589 (tt0) REVERT: F 199 SER cc_start: 0.9328 (OUTLIER) cc_final: 0.8807 (p) REVERT: F 263 MET cc_start: 0.8298 (mmp) cc_final: 0.7868 (mmm) REVERT: F 279 MET cc_start: 0.8152 (mmm) cc_final: 0.7694 (mmm) REVERT: F 743 MET cc_start: 0.8760 (mmt) cc_final: 0.8376 (mmp) REVERT: F 746 MET cc_start: 0.8091 (ttm) cc_final: 0.6178 (ttm) REVERT: F 751 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9085 (tppp) REVERT: F 848 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.8567 (t-90) REVERT: a 142 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.7876 (p) REVERT: a 252 ARG cc_start: 0.8000 (mmm-85) cc_final: 0.7763 (mtp85) REVERT: b 84 MET cc_start: 0.8491 (ptp) cc_final: 0.8028 (pmm) REVERT: b 488 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: c 219 MET cc_start: 0.8478 (mtm) cc_final: 0.8121 (mtm) REVERT: d 24 TRP cc_start: 0.8548 (p-90) cc_final: 0.8172 (p-90) REVERT: d 46 THR cc_start: 0.8903 (p) cc_final: 0.8603 (t) REVERT: d 54 GLN cc_start: 0.9391 (tm-30) cc_final: 0.9135 (tm-30) REVERT: d 161 ARG cc_start: 0.9081 (ttp-110) cc_final: 0.8834 (ttp-110) REVERT: e 20 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8750 (pt) REVERT: e 172 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9062 (mt) REVERT: e 174 THR cc_start: 0.9616 (m) cc_final: 0.9392 (p) REVERT: f 746 MET cc_start: 0.7843 (mmp) cc_final: 0.7254 (mmm) REVERT: f 773 GLN cc_start: 0.9425 (mp10) cc_final: 0.9129 (mp10) REVERT: f 823 TYR cc_start: 0.7957 (m-80) cc_final: 0.7596 (m-80) outliers start: 91 outliers final: 53 residues processed: 377 average time/residue: 0.2577 time to fit residues: 158.3213 Evaluate side-chains 354 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 288 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 119 HIS Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 730 PHE Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 765 TYR Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 293 ASN Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 475 SER Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain b residue 488 GLN Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 216 ASP Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 108 LEU Chi-restraints excluded: chain e residue 172 LEU Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 767 ILE Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 776 GLU Chi-restraints excluded: chain f residue 820 LEU Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 895 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 38 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 188 optimal weight: 0.0370 chunk 8 optimal weight: 0.0370 chunk 231 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 413 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.079819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051701 restraints weight = 231047.168| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 5.27 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40288 Z= 0.113 Angle : 0.544 16.455 54991 Z= 0.278 Chirality : 0.039 0.201 6102 Planarity : 0.003 0.059 6544 Dihedral : 16.750 76.979 6467 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.03 % Allowed : 21.26 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.13), residues: 4461 helix: 2.70 (0.13), residues: 1798 sheet: 0.69 (0.19), residues: 750 loop : -0.21 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 502 TYR 0.021 0.001 TYR f 698 PHE 0.026 0.001 PHE e 162 TRP 0.025 0.001 TRP F 738 HIS 0.024 0.001 HIS F 119 Details of bonding type rmsd covalent geometry : bond 0.00251 (40287) covalent geometry : angle 0.54443 (54991) hydrogen bonds : bond 0.03161 ( 1987) hydrogen bonds : angle 4.13791 ( 5519) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 310 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.6753 (t80) REVERT: B 20 MET cc_start: 0.7880 (tpp) cc_final: 0.7172 (tpp) REVERT: B 288 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8319 (t0) REVERT: C 98 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8435 (m-30) REVERT: D 3 ARG cc_start: 0.8494 (ptm160) cc_final: 0.7851 (ptm160) REVERT: D 10 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8401 (tp) REVERT: D 52 ILE cc_start: 0.8807 (tt) cc_final: 0.8591 (pt) REVERT: D 71 ARG cc_start: 0.9109 (mtp-110) cc_final: 0.8796 (mtt-85) REVERT: D 192 ARG cc_start: 0.9283 (mpt180) cc_final: 0.8642 (mmm160) REVERT: E 54 GLN cc_start: 0.9277 (tm-30) cc_final: 0.9056 (tm-30) REVERT: E 103 ASP cc_start: 0.8828 (t0) cc_final: 0.8357 (t0) REVERT: E 175 ASP cc_start: 0.9324 (OUTLIER) cc_final: 0.8957 (p0) REVERT: F 44 ASP cc_start: 0.9219 (t70) cc_final: 0.8903 (t70) REVERT: F 95 GLU cc_start: 0.8843 (tt0) cc_final: 0.8595 (tt0) REVERT: F 279 MET cc_start: 0.8101 (mmm) cc_final: 0.7654 (mmm) REVERT: F 430 MET cc_start: 0.8915 (mtp) cc_final: 0.8527 (mtp) REVERT: F 439 LYS cc_start: 0.9175 (mmmm) cc_final: 0.8865 (mtmt) REVERT: F 569 MET cc_start: 0.9314 (mtp) cc_final: 0.8482 (mmm) REVERT: F 746 MET cc_start: 0.8079 (ttm) cc_final: 0.7622 (ttm) REVERT: F 848 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.8591 (t-90) REVERT: a 142 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7863 (p) REVERT: a 252 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7732 (mtp85) REVERT: a 379 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8747 (m) REVERT: c 219 MET cc_start: 0.8468 (mtm) cc_final: 0.8094 (mtm) REVERT: d 24 TRP cc_start: 0.8599 (p-90) cc_final: 0.8228 (p-90) REVERT: d 46 THR cc_start: 0.8903 (p) cc_final: 0.8582 (t) REVERT: d 54 GLN cc_start: 0.9386 (tm-30) cc_final: 0.9110 (tm-30) REVERT: d 59 MET cc_start: 0.8095 (tpp) cc_final: 0.7344 (mmt) REVERT: d 138 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8787 (pp30) REVERT: d 161 ARG cc_start: 0.9096 (ttp-110) cc_final: 0.8849 (ttp-110) REVERT: e 20 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8701 (pt) REVERT: e 89 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8036 (p) REVERT: e 172 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9025 (mt) REVERT: e 174 THR cc_start: 0.9599 (m) cc_final: 0.9372 (p) REVERT: f 746 MET cc_start: 0.7664 (mmp) cc_final: 0.7262 (mmm) REVERT: f 770 ASP cc_start: 0.9371 (OUTLIER) cc_final: 0.9112 (t0) REVERT: f 773 GLN cc_start: 0.9421 (mp10) cc_final: 0.9116 (mp10) REVERT: f 823 TYR cc_start: 0.8028 (m-80) cc_final: 0.7735 (m-80) REVERT: f 834 GLU cc_start: 0.9320 (pm20) cc_final: 0.9108 (tm-30) outliers start: 82 outliers final: 52 residues processed: 381 average time/residue: 0.2657 time to fit residues: 165.4888 Evaluate side-chains 365 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 301 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 730 PHE Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 765 TYR Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 219 ASP Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain a residue 281 LEU Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 379 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 256 ASN Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 64 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 216 ASP Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 89 SER Chi-restraints excluded: chain e residue 108 LEU Chi-restraints excluded: chain e residue 128 CYS Chi-restraints excluded: chain e residue 172 LEU Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 776 GLU Chi-restraints excluded: chain f residue 820 LEU Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 895 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 16 optimal weight: 8.9990 chunk 305 optimal weight: 3.9990 chunk 362 optimal weight: 0.9980 chunk 225 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 363 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 424 optimal weight: 0.0770 chunk 391 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 158 ASN ** F 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 360 HIS b 22 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.079261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.051064 restraints weight = 214263.574| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 5.10 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40288 Z= 0.144 Angle : 0.550 13.549 54991 Z= 0.281 Chirality : 0.039 0.210 6102 Planarity : 0.003 0.060 6544 Dihedral : 16.759 76.666 6467 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.96 % Allowed : 21.56 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.13), residues: 4461 helix: 2.63 (0.13), residues: 1799 sheet: 0.66 (0.19), residues: 761 loop : -0.19 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG e 153 TYR 0.020 0.001 TYR f 801 PHE 0.026 0.001 PHE b 107 TRP 0.017 0.001 TRP F 738 HIS 0.005 0.001 HIS F 282 Details of bonding type rmsd covalent geometry : bond 0.00329 (40287) covalent geometry : angle 0.54973 (54991) hydrogen bonds : bond 0.03222 ( 1987) hydrogen bonds : angle 4.16380 ( 5519) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 304 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.6818 (t80) REVERT: B 20 MET cc_start: 0.7846 (tpp) cc_final: 0.7138 (tpp) REVERT: B 148 ASP cc_start: 0.9446 (m-30) cc_final: 0.9044 (p0) REVERT: B 288 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8322 (t0) REVERT: C 98 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8414 (m-30) REVERT: D 10 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8436 (tp) REVERT: D 52 ILE cc_start: 0.8868 (tt) cc_final: 0.8649 (pt) REVERT: D 71 ARG cc_start: 0.9116 (mtp-110) cc_final: 0.8815 (mtt-85) REVERT: D 150 ARG cc_start: 0.9535 (tmm-80) cc_final: 0.9099 (ttp80) REVERT: D 192 ARG cc_start: 0.9285 (mpt180) cc_final: 0.8634 (mmm160) REVERT: E 103 ASP cc_start: 0.8920 (t0) cc_final: 0.8501 (t0) REVERT: E 175 ASP cc_start: 0.9299 (OUTLIER) cc_final: 0.8912 (p0) REVERT: F 44 ASP cc_start: 0.9233 (t70) cc_final: 0.8919 (t70) REVERT: F 95 GLU cc_start: 0.8849 (tt0) cc_final: 0.8584 (tt0) REVERT: F 199 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.8825 (p) REVERT: F 279 MET cc_start: 0.8111 (mmm) cc_final: 0.7657 (mmm) REVERT: F 439 LYS cc_start: 0.9176 (mmmm) cc_final: 0.8710 (mtpp) REVERT: F 569 MET cc_start: 0.9306 (mtp) cc_final: 0.8506 (mmm) REVERT: F 746 MET cc_start: 0.8063 (ttm) cc_final: 0.7573 (ttm) REVERT: F 848 HIS cc_start: 0.8884 (OUTLIER) cc_final: 0.8596 (t-90) REVERT: a 134 MET cc_start: 0.9241 (tmm) cc_final: 0.8994 (tmm) REVERT: a 142 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7861 (p) REVERT: a 252 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7635 (mtm180) REVERT: a 379 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8743 (m) REVERT: a 462 MET cc_start: 0.9035 (tpp) cc_final: 0.8758 (tpp) REVERT: b 84 MET cc_start: 0.8509 (ptp) cc_final: 0.8131 (pmm) REVERT: c 219 MET cc_start: 0.8493 (mtm) cc_final: 0.8096 (mtm) REVERT: d 24 TRP cc_start: 0.8676 (p-90) cc_final: 0.8201 (p-90) REVERT: d 46 THR cc_start: 0.8980 (p) cc_final: 0.8695 (t) REVERT: d 54 GLN cc_start: 0.9400 (tm-30) cc_final: 0.9130 (tm-30) REVERT: d 144 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9186 (tp) REVERT: d 161 ARG cc_start: 0.9121 (ttp-110) cc_final: 0.8903 (ttp-110) REVERT: e 20 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8698 (pt) REVERT: e 89 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8041 (p) REVERT: e 172 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9029 (mt) REVERT: e 174 THR cc_start: 0.9604 (m) cc_final: 0.9380 (p) REVERT: f 746 MET cc_start: 0.7687 (mmp) cc_final: 0.7340 (mmm) REVERT: f 770 ASP cc_start: 0.9382 (OUTLIER) cc_final: 0.9110 (t0) REVERT: f 773 GLN cc_start: 0.9440 (mp10) cc_final: 0.9134 (mp10) REVERT: f 823 TYR cc_start: 0.8134 (m-80) cc_final: 0.7804 (m-80) outliers start: 79 outliers final: 61 residues processed: 369 average time/residue: 0.2494 time to fit residues: 150.2421 Evaluate side-chains 366 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 291 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 765 TYR Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 219 ASP Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain a residue 281 LEU Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 379 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 475 SER Chi-restraints excluded: chain b residue 256 ASN Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 64 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 216 ASP Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 89 SER Chi-restraints excluded: chain e residue 108 LEU Chi-restraints excluded: chain e residue 128 CYS Chi-restraints excluded: chain e residue 172 LEU Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 767 ILE Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 776 GLU Chi-restraints excluded: chain f residue 820 LEU Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 895 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 282 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 374 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 315 optimal weight: 0.7980 chunk 395 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.079142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050636 restraints weight = 209654.039| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 5.08 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40288 Z= 0.126 Angle : 0.557 13.780 54991 Z= 0.283 Chirality : 0.039 0.219 6102 Planarity : 0.003 0.059 6544 Dihedral : 16.745 76.600 6467 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.98 % Allowed : 22.00 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.13), residues: 4461 helix: 2.63 (0.13), residues: 1793 sheet: 0.67 (0.19), residues: 765 loop : -0.19 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG e 153 TYR 0.021 0.001 TYR f 801 PHE 0.028 0.001 PHE e 162 TRP 0.016 0.001 TRP F 738 HIS 0.005 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00285 (40287) covalent geometry : angle 0.55748 (54991) hydrogen bonds : bond 0.03146 ( 1987) hydrogen bonds : angle 4.12448 ( 5519) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 300 time to evaluate : 1.642 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 233 PHE cc_start: 0.8620 (m-80) cc_final: 0.8395 (m-10) REVERT: A 409 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.6697 (t80) REVERT: B 20 MET cc_start: 0.7777 (tpp) cc_final: 0.7039 (tpp) REVERT: B 148 ASP cc_start: 0.9440 (m-30) cc_final: 0.9035 (p0) REVERT: B 210 MET cc_start: 0.9387 (ppp) cc_final: 0.8821 (ppp) REVERT: B 288 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8341 (t0) REVERT: D 10 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8432 (tp) REVERT: D 52 ILE cc_start: 0.8886 (tt) cc_final: 0.8671 (pt) REVERT: D 59 MET cc_start: 0.7727 (pmm) cc_final: 0.7145 (pmm) REVERT: D 71 ARG cc_start: 0.9084 (mtp-110) cc_final: 0.8769 (mtt-85) REVERT: D 192 ARG cc_start: 0.9300 (mpt180) cc_final: 0.8647 (mmm160) REVERT: E 103 ASP cc_start: 0.8951 (t0) cc_final: 0.8543 (t0) REVERT: E 175 ASP cc_start: 0.9287 (OUTLIER) cc_final: 0.8888 (p0) REVERT: F 44 ASP cc_start: 0.9217 (t70) cc_final: 0.8905 (t70) REVERT: F 95 GLU cc_start: 0.8839 (tt0) cc_final: 0.8555 (tt0) REVERT: F 199 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.8827 (p) REVERT: F 279 MET cc_start: 0.8097 (mmm) cc_final: 0.7639 (mmm) REVERT: F 430 MET cc_start: 0.8841 (mtp) cc_final: 0.8487 (mtp) REVERT: F 439 LYS cc_start: 0.9170 (mmmm) cc_final: 0.8685 (mtpp) REVERT: F 569 MET cc_start: 0.9289 (mtp) cc_final: 0.8493 (mmm) REVERT: F 746 MET cc_start: 0.8036 (ttm) cc_final: 0.7540 (ttm) REVERT: F 848 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8604 (t-90) REVERT: a 134 MET cc_start: 0.9290 (tmm) cc_final: 0.9077 (tmm) REVERT: a 142 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.7886 (p) REVERT: a 252 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7634 (mtm180) REVERT: a 379 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8740 (m) REVERT: a 462 MET cc_start: 0.8990 (tpp) cc_final: 0.8765 (tpp) REVERT: b 84 MET cc_start: 0.8542 (ptp) cc_final: 0.8159 (pmm) REVERT: c 219 MET cc_start: 0.8488 (mtm) cc_final: 0.8082 (mtm) REVERT: d 24 TRP cc_start: 0.8683 (p-90) cc_final: 0.8209 (p-90) REVERT: d 46 THR cc_start: 0.9006 (p) cc_final: 0.8736 (t) REVERT: d 54 GLN cc_start: 0.9406 (tm-30) cc_final: 0.9129 (tm-30) REVERT: d 144 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9194 (tp) REVERT: d 161 ARG cc_start: 0.9126 (ttp-110) cc_final: 0.8900 (ttp-110) REVERT: e 20 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8686 (pt) REVERT: e 89 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8048 (p) REVERT: e 172 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9021 (mt) REVERT: e 174 THR cc_start: 0.9599 (m) cc_final: 0.9375 (p) REVERT: f 746 MET cc_start: 0.7636 (mmp) cc_final: 0.7350 (mmm) REVERT: f 770 ASP cc_start: 0.9360 (OUTLIER) cc_final: 0.9080 (t0) REVERT: f 773 GLN cc_start: 0.9451 (mp10) cc_final: 0.9235 (mp10) REVERT: f 803 TYR cc_start: 0.8605 (m-80) cc_final: 0.8012 (m-80) REVERT: f 823 TYR cc_start: 0.8148 (m-80) cc_final: 0.7832 (m-80) REVERT: f 834 GLU cc_start: 0.9330 (pm20) cc_final: 0.9067 (tm-30) outliers start: 80 outliers final: 55 residues processed: 368 average time/residue: 0.2613 time to fit residues: 157.4190 Evaluate side-chains 363 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 295 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 730 PHE Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 765 TYR Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 219 ASP Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain a residue 281 LEU Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 379 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 475 SER Chi-restraints excluded: chain b residue 256 ASN Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 64 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 170 SER Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 89 SER Chi-restraints excluded: chain e residue 108 LEU Chi-restraints excluded: chain e residue 128 CYS Chi-restraints excluded: chain e residue 172 LEU Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 767 ILE Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 820 LEU Chi-restraints excluded: chain f residue 895 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 133 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 119 HIS ** F 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.078838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.050655 restraints weight = 205247.376| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 5.00 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40288 Z= 0.169 Angle : 0.575 14.590 54991 Z= 0.293 Chirality : 0.039 0.225 6102 Planarity : 0.003 0.059 6544 Dihedral : 16.813 76.236 6467 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.98 % Allowed : 22.10 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.13), residues: 4461 helix: 2.59 (0.13), residues: 1795 sheet: 0.63 (0.19), residues: 765 loop : -0.18 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG e 153 TYR 0.020 0.001 TYR f 801 PHE 0.031 0.001 PHE e 162 TRP 0.017 0.001 TRP F 738 HIS 0.007 0.001 HIS F 282 Details of bonding type rmsd covalent geometry : bond 0.00387 (40287) covalent geometry : angle 0.57499 (54991) hydrogen bonds : bond 0.03317 ( 1987) hydrogen bonds : angle 4.18555 ( 5519) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 295 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8152 (tpp) cc_final: 0.7900 (tpp) REVERT: A 409 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.6892 (t80) REVERT: A 453 MET cc_start: 0.8688 (tpp) cc_final: 0.8480 (mmm) REVERT: B 64 THR cc_start: 0.7040 (OUTLIER) cc_final: 0.6818 (m) REVERT: B 148 ASP cc_start: 0.9437 (m-30) cc_final: 0.9032 (p0) REVERT: B 288 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8359 (t0) REVERT: C 98 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8437 (m-30) REVERT: D 10 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8456 (tp) REVERT: D 59 MET cc_start: 0.7719 (pmm) cc_final: 0.7085 (pmm) REVERT: D 71 ARG cc_start: 0.9094 (mtp-110) cc_final: 0.8790 (mtt-85) REVERT: D 155 TRP cc_start: 0.9053 (OUTLIER) cc_final: 0.8754 (t60) REVERT: D 192 ARG cc_start: 0.9303 (mpt180) cc_final: 0.8638 (mmm160) REVERT: E 103 ASP cc_start: 0.8951 (t0) cc_final: 0.8587 (t0) REVERT: E 175 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.8897 (p0) REVERT: F 44 ASP cc_start: 0.9233 (t70) cc_final: 0.8926 (t70) REVERT: F 95 GLU cc_start: 0.8838 (tt0) cc_final: 0.8558 (tt0) REVERT: F 199 SER cc_start: 0.9360 (OUTLIER) cc_final: 0.8867 (p) REVERT: F 279 MET cc_start: 0.8122 (mmm) cc_final: 0.7658 (mmm) REVERT: F 439 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8861 (mttp) REVERT: F 743 MET cc_start: 0.8995 (tpp) cc_final: 0.8571 (mmm) REVERT: F 746 MET cc_start: 0.8024 (ttm) cc_final: 0.7583 (ttm) REVERT: F 848 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8555 (t-90) REVERT: a 134 MET cc_start: 0.9363 (tmm) cc_final: 0.9133 (tmm) REVERT: a 142 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7866 (p) REVERT: a 252 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7654 (mtm180) REVERT: a 379 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8741 (m) REVERT: b 84 MET cc_start: 0.8589 (ptp) cc_final: 0.8191 (pmm) REVERT: c 219 MET cc_start: 0.8503 (mtm) cc_final: 0.8137 (mtm) REVERT: d 24 TRP cc_start: 0.8728 (p-90) cc_final: 0.8266 (p-90) REVERT: d 46 THR cc_start: 0.8969 (p) cc_final: 0.8693 (t) REVERT: d 54 GLN cc_start: 0.9402 (tm-30) cc_final: 0.9132 (tm-30) REVERT: d 138 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8824 (pp30) REVERT: d 144 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9206 (tp) REVERT: d 161 ARG cc_start: 0.9152 (ttp-110) cc_final: 0.8340 (ptp-170) REVERT: e 89 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8077 (p) REVERT: e 172 LEU cc_start: 0.9395 (mt) cc_final: 0.9014 (mt) REVERT: e 174 THR cc_start: 0.9619 (m) cc_final: 0.9393 (p) REVERT: f 746 MET cc_start: 0.7647 (mmp) cc_final: 0.7365 (mmm) REVERT: f 770 ASP cc_start: 0.9421 (OUTLIER) cc_final: 0.9189 (t0) REVERT: f 773 GLN cc_start: 0.9551 (mp10) cc_final: 0.9234 (mp10) REVERT: f 823 TYR cc_start: 0.8195 (m-80) cc_final: 0.7902 (m-80) REVERT: f 834 GLU cc_start: 0.9357 (pm20) cc_final: 0.9057 (tm-30) outliers start: 80 outliers final: 56 residues processed: 363 average time/residue: 0.2590 time to fit residues: 153.8471 Evaluate side-chains 356 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 286 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 155 TRP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 730 PHE Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 765 TYR Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 219 ASP Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain a residue 281 LEU Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 379 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 475 SER Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 64 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 170 SER Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 89 SER Chi-restraints excluded: chain e residue 108 LEU Chi-restraints excluded: chain e residue 128 CYS Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 767 ILE Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 820 LEU Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 895 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 31 optimal weight: 0.6980 chunk 320 optimal weight: 0.8980 chunk 405 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 387 optimal weight: 3.9990 chunk 312 optimal weight: 0.7980 chunk 357 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 305 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 GLN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.078964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050079 restraints weight = 233328.764| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 5.39 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40288 Z= 0.125 Angle : 0.567 15.706 54991 Z= 0.287 Chirality : 0.039 0.231 6102 Planarity : 0.003 0.059 6544 Dihedral : 16.808 77.983 6467 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.71 % Allowed : 22.25 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.13), residues: 4461 helix: 2.56 (0.13), residues: 1793 sheet: 0.64 (0.19), residues: 765 loop : -0.18 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 502 TYR 0.022 0.001 TYR f 801 PHE 0.028 0.001 PHE e 162 TRP 0.015 0.001 TRP F 738 HIS 0.003 0.000 HIS F 215 Details of bonding type rmsd covalent geometry : bond 0.00283 (40287) covalent geometry : angle 0.56690 (54991) hydrogen bonds : bond 0.03164 ( 1987) hydrogen bonds : angle 4.13937 ( 5519) Misc. bond : bond 0.00010 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 298 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.6713 (t80) REVERT: A 453 MET cc_start: 0.8653 (tpp) cc_final: 0.8444 (mmm) REVERT: B 64 THR cc_start: 0.7096 (OUTLIER) cc_final: 0.6870 (m) REVERT: B 148 ASP cc_start: 0.9440 (m-30) cc_final: 0.9027 (p0) REVERT: B 288 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8333 (t0) REVERT: B 389 MET cc_start: 0.9134 (mtt) cc_final: 0.8916 (mtt) REVERT: D 10 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8438 (tp) REVERT: D 71 ARG cc_start: 0.9079 (mtp-110) cc_final: 0.8769 (mtt-85) REVERT: D 155 TRP cc_start: 0.9031 (OUTLIER) cc_final: 0.8737 (t60) REVERT: D 192 ARG cc_start: 0.9307 (mpt180) cc_final: 0.8642 (mmm160) REVERT: E 103 ASP cc_start: 0.8951 (t0) cc_final: 0.8604 (t0) REVERT: E 175 ASP cc_start: 0.9279 (OUTLIER) cc_final: 0.8865 (p0) REVERT: F 44 ASP cc_start: 0.9221 (t70) cc_final: 0.8975 (t70) REVERT: F 95 GLU cc_start: 0.8843 (tt0) cc_final: 0.8525 (tt0) REVERT: F 279 MET cc_start: 0.8034 (mmm) cc_final: 0.7593 (mmm) REVERT: F 439 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8860 (mttp) REVERT: F 746 MET cc_start: 0.7994 (ttm) cc_final: 0.7496 (ttm) REVERT: F 848 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8534 (t-90) REVERT: a 142 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7876 (p) REVERT: a 379 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8774 (m) REVERT: b 84 MET cc_start: 0.8644 (ptp) cc_final: 0.8251 (pmm) REVERT: c 219 MET cc_start: 0.8510 (mtm) cc_final: 0.8105 (mtm) REVERT: d 3 ARG cc_start: 0.8591 (ptm160) cc_final: 0.8058 (ptm160) REVERT: d 24 TRP cc_start: 0.8735 (p-90) cc_final: 0.8272 (p-90) REVERT: d 46 THR cc_start: 0.9001 (p) cc_final: 0.8731 (t) REVERT: d 54 GLN cc_start: 0.9420 (tm-30) cc_final: 0.9159 (tm-30) REVERT: d 138 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8792 (pp30) REVERT: d 144 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9203 (tp) REVERT: d 161 ARG cc_start: 0.9125 (ttp-110) cc_final: 0.8335 (ptp-170) REVERT: e 20 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8713 (pt) REVERT: e 89 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8088 (p) REVERT: e 172 LEU cc_start: 0.9393 (mt) cc_final: 0.9015 (mt) REVERT: e 174 THR cc_start: 0.9618 (m) cc_final: 0.9390 (p) REVERT: f 746 MET cc_start: 0.7592 (mmp) cc_final: 0.7331 (mmm) REVERT: f 770 ASP cc_start: 0.9407 (OUTLIER) cc_final: 0.9140 (t0) REVERT: f 773 GLN cc_start: 0.9549 (mp10) cc_final: 0.9234 (mp10) REVERT: f 823 TYR cc_start: 0.8296 (m-80) cc_final: 0.7991 (m-80) REVERT: f 834 GLU cc_start: 0.9381 (pm20) cc_final: 0.9067 (tm-30) outliers start: 69 outliers final: 53 residues processed: 358 average time/residue: 0.2601 time to fit residues: 151.8245 Evaluate side-chains 359 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 155 TRP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 730 PHE Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 765 TYR Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 219 ASP Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain a residue 281 LEU Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 379 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 475 SER Chi-restraints excluded: chain b residue 354 ARG Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 64 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 170 SER Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 89 SER Chi-restraints excluded: chain e residue 108 LEU Chi-restraints excluded: chain e residue 128 CYS Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 767 ILE Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 820 LEU Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 895 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 389 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 398 optimal weight: 8.9990 chunk 396 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 308 optimal weight: 0.9980 chunk 429 optimal weight: 2.9990 chunk 148 optimal weight: 0.0470 chunk 86 optimal weight: 0.0000 chunk 221 optimal weight: 5.9990 overall best weight: 0.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN F 50 HIS ** F 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.079179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050605 restraints weight = 194781.960| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.98 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40288 Z= 0.119 Angle : 0.563 15.706 54991 Z= 0.286 Chirality : 0.039 0.238 6102 Planarity : 0.003 0.064 6544 Dihedral : 16.783 79.540 6467 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.69 % Allowed : 22.53 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.13), residues: 4461 helix: 2.55 (0.13), residues: 1793 sheet: 0.64 (0.19), residues: 767 loop : -0.16 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 502 TYR 0.022 0.001 TYR f 801 PHE 0.028 0.001 PHE b 107 TRP 0.015 0.001 TRP F 805 HIS 0.007 0.001 HIS F 282 Details of bonding type rmsd covalent geometry : bond 0.00268 (40287) covalent geometry : angle 0.56304 (54991) hydrogen bonds : bond 0.03134 ( 1987) hydrogen bonds : angle 4.10843 ( 5519) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13322.30 seconds wall clock time: 228 minutes 30.87 seconds (13710.87 seconds total)