Starting phenix.real_space_refine on Fri Mar 6 22:54:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yo4_33981/03_2026/7yo4_33981.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yo4_33981/03_2026/7yo4_33981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yo4_33981/03_2026/7yo4_33981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yo4_33981/03_2026/7yo4_33981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yo4_33981/03_2026/7yo4_33981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yo4_33981/03_2026/7yo4_33981.map" } resolution = 3.9 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 232 5.16 5 C 22952 2.51 5 N 6004 2.21 5 O 6372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35560 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 7114 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 28, 'TRANS': 865} Chain breaks: 3 Chain: "B" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1776 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 21, 'TRANS': 220} Chain: "C" Number of atoms: 7114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 7114 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 28, 'TRANS': 865} Chain breaks: 3 Chain: "D" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1776 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 21, 'TRANS': 220} Chain: "E" Number of atoms: 7114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 7114 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 28, 'TRANS': 865} Chain breaks: 3 Chain: "F" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1776 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 21, 'TRANS': 220} Chain: "G" Number of atoms: 7114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 7114 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 28, 'TRANS': 865} Chain breaks: 3 Chain: "H" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1776 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 21, 'TRANS': 220} Time building chain proxies: 7.59, per 1000 atoms: 0.21 Number of scatterers: 35560 At special positions: 0 Unit cell: (167.328, 168.324, 186.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 232 16.00 O 6372 8.00 N 6004 7.00 C 22952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 57 " distance=2.05 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 57 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS F 47 " - pdb=" SG CYS F 57 " distance=2.03 Simple disulfide: pdb=" SG CYS F 205 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 47 " - pdb=" SG CYS H 57 " distance=2.03 Simple disulfide: pdb=" SG CYS H 205 " - pdb=" SG CYS H 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.5 seconds 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8568 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 31 sheets defined 47.7% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 removed outlier: 3.654A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 109 through 135 removed outlier: 4.465A pdb=" N SER A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 171 removed outlier: 3.898A pdb=" N GLN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 180 through 197 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.831A pdb=" N LEU A 209 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 318 Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.646A pdb=" N HIS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 removed outlier: 3.518A pdb=" N VAL A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.715A pdb=" N ALA A 467 " --> pdb=" O HIS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.856A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.705A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 601 through 606' Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.858A pdb=" N TYR A 611 " --> pdb=" O ALA A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.980A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.831A pdb=" N ALA A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 759 through 767 removed outlier: 3.681A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 793 removed outlier: 3.531A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 797 removed outlier: 3.550A pdb=" N CYS A 797 " --> pdb=" O ILE A 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 814 through 816 No H-bonds generated for 'chain 'A' and resid 814 through 816' Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.673A pdb=" N VAL A 888 " --> pdb=" O ASN A 884 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN A 889 " --> pdb=" O ASP A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 889' Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 917 through 930 removed outlier: 4.047A pdb=" N ASP A 921 " --> pdb=" O VAL A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 3.860A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 removed outlier: 3.723A pdb=" N GLU A 950 " --> pdb=" O THR A 946 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 973 removed outlier: 3.889A pdb=" N ASP A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 removed outlier: 3.554A pdb=" N GLY A 991 " --> pdb=" O PHE A 987 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 992' Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 183 through 190 removed outlier: 4.317A pdb=" N LEU B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 219 removed outlier: 4.596A pdb=" N LEU B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.561A pdb=" N ALA B 223 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 284 removed outlier: 4.117A pdb=" N VAL B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'C' and resid 21 through 34 removed outlier: 3.680A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 109 through 135 removed outlier: 4.458A pdb=" N SER C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 171 removed outlier: 3.838A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 199 Proline residue: C 191 - end of helix removed outlier: 4.625A pdb=" N TYR C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.655A pdb=" N LEU C 209 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 211 " --> pdb=" O PHE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.568A pdb=" N ILE C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 259 Processing helix chain 'C' and resid 261 through 265 removed outlier: 3.704A pdb=" N ASN C 265 " --> pdb=" O PRO C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 318 Processing helix chain 'C' and resid 319 through 328 Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 removed outlier: 3.685A pdb=" N HIS C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.709A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 Processing helix chain 'C' and resid 466 through 471 removed outlier: 3.734A pdb=" N LEU C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 466 through 471' Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.017A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.737A pdb=" N LYS C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 610 Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 699 through 704 removed outlier: 3.583A pdb=" N ILE C 704 " --> pdb=" O GLU C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 742 Proline residue: C 740 - end of helix Processing helix chain 'C' and resid 747 through 751 Processing helix chain 'C' and resid 759 through 767 Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 785 through 793 Processing helix chain 'C' and resid 813 through 816 removed outlier: 4.070A pdb=" N GLN C 816 " --> pdb=" O THR C 813 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 813 through 816' Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 872 through 876 removed outlier: 3.618A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 891 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 917 through 930 removed outlier: 4.059A pdb=" N ASP C 921 " --> pdb=" O VAL C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 942 removed outlier: 4.039A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 removed outlier: 3.763A pdb=" N GLU C 950 " --> pdb=" O THR C 946 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 951 " --> pdb=" O PRO C 947 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 952 " --> pdb=" O GLU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 972 removed outlier: 3.604A pdb=" N ARG C 972 " --> pdb=" O THR C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 Processing helix chain 'C' and resid 995 through 1007 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 183 through 190 removed outlier: 4.279A pdb=" N LEU D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 258 through 284 removed outlier: 4.218A pdb=" N VAL D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR D 267 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLY D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Proline residue: D 270 - end of helix Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.673A pdb=" N PHE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 106 Processing helix chain 'E' and resid 109 through 135 removed outlier: 3.559A pdb=" N ARG E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 171 removed outlier: 3.969A pdb=" N GLN E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 197 Proline residue: E 191 - end of helix Processing helix chain 'E' and resid 206 through 215 removed outlier: 3.969A pdb=" N LEU E 209 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG E 210 " --> pdb=" O ARG E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.771A pdb=" N GLN E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 259 Processing helix chain 'E' and resid 261 through 265 Processing helix chain 'E' and resid 273 through 286 Processing helix chain 'E' and resid 297 through 318 Processing helix chain 'E' and resid 318 through 328 removed outlier: 4.629A pdb=" N ILE E 322 " --> pdb=" O TYR E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 364 Processing helix chain 'E' and resid 384 through 394 removed outlier: 3.614A pdb=" N HIS E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 414 removed outlier: 3.521A pdb=" N VAL E 414 " --> pdb=" O ASP E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 451 removed outlier: 3.547A pdb=" N GLU E 436 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 472 removed outlier: 3.920A pdb=" N ALA E 467 " --> pdb=" O HIS E 464 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE E 472 " --> pdb=" O LEU E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 500 Processing helix chain 'E' and resid 502 through 512 Processing helix chain 'E' and resid 523 through 533 removed outlier: 3.933A pdb=" N TYR E 527 " --> pdb=" O THR E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 546 Processing helix chain 'E' and resid 549 through 562 Processing helix chain 'E' and resid 601 through 606 removed outlier: 3.661A pdb=" N VAL E 605 " --> pdb=" O ASP E 601 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS E 606 " --> pdb=" O ALA E 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 601 through 606' Processing helix chain 'E' and resid 607 through 609 No H-bonds generated for 'chain 'E' and resid 607 through 609' Processing helix chain 'E' and resid 621 through 626 Processing helix chain 'E' and resid 706 through 713 Processing helix chain 'E' and resid 734 through 742 Proline residue: E 740 - end of helix Processing helix chain 'E' and resid 759 through 767 Processing helix chain 'E' and resid 768 through 770 No H-bonds generated for 'chain 'E' and resid 768 through 770' Processing helix chain 'E' and resid 785 through 792 removed outlier: 3.609A pdb=" N LEU E 789 " --> pdb=" O SER E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 793 through 797 removed outlier: 3.575A pdb=" N CYS E 797 " --> pdb=" O ILE E 794 " (cutoff:3.500A) Processing helix chain 'E' and resid 813 through 816 removed outlier: 3.809A pdb=" N GLN E 816 " --> pdb=" O THR E 813 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 813 through 816' Processing helix chain 'E' and resid 817 through 829 Processing helix chain 'E' and resid 885 through 891 Processing helix chain 'E' and resid 906 through 911 Processing helix chain 'E' and resid 917 through 930 removed outlier: 4.170A pdb=" N ASP E 921 " --> pdb=" O VAL E 917 " (cutoff:3.500A) Processing helix chain 'E' and resid 931 through 942 removed outlier: 4.055A pdb=" N THR E 935 " --> pdb=" O ASP E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 957 removed outlier: 3.669A pdb=" N GLU E 950 " --> pdb=" O THR E 946 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU E 956 " --> pdb=" O LEU E 952 " (cutoff:3.500A) Processing helix chain 'E' and resid 965 through 972 Processing helix chain 'E' and resid 987 through 992 Processing helix chain 'E' and resid 995 through 1007 removed outlier: 3.621A pdb=" N LEU E 999 " --> pdb=" O CYS E 995 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.774A pdb=" N GLY F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 removed outlier: 4.193A pdb=" N LEU F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 209 through 219 Processing helix chain 'F' and resid 220 through 224 Processing helix chain 'F' and resid 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing helix chain 'F' and resid 258 through 283 removed outlier: 4.682A pdb=" N VAL F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N THR F 267 " --> pdb=" O ALA F 263 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY F 269 " --> pdb=" O VAL F 265 " (cutoff:3.500A) Proline residue: F 270 - end of helix Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.603A pdb=" N PHE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 106 Processing helix chain 'G' and resid 109 through 135 removed outlier: 4.328A pdb=" N SER G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 171 removed outlier: 4.095A pdb=" N GLN G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 179 Processing helix chain 'G' and resid 180 through 199 Proline residue: G 191 - end of helix removed outlier: 4.610A pdb=" N TYR G 198 " --> pdb=" O PHE G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 212 removed outlier: 4.039A pdb=" N LEU G 209 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG G 210 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 Processing helix chain 'G' and resid 229 through 259 Processing helix chain 'G' and resid 273 through 286 Processing helix chain 'G' and resid 297 through 318 Processing helix chain 'G' and resid 318 through 328 removed outlier: 4.295A pdb=" N ILE G 322 " --> pdb=" O TYR G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 364 Processing helix chain 'G' and resid 384 through 394 removed outlier: 3.504A pdb=" N HIS G 394 " --> pdb=" O LEU G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 414 Processing helix chain 'G' and resid 432 through 451 Processing helix chain 'G' and resid 462 through 465 Processing helix chain 'G' and resid 466 through 471 removed outlier: 4.016A pdb=" N LEU G 470 " --> pdb=" O LYS G 466 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN G 471 " --> pdb=" O ALA G 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 466 through 471' Processing helix chain 'G' and resid 486 through 500 Processing helix chain 'G' and resid 502 through 512 Processing helix chain 'G' and resid 523 through 533 removed outlier: 4.005A pdb=" N TYR G 527 " --> pdb=" O THR G 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 546 Processing helix chain 'G' and resid 549 through 560 Processing helix chain 'G' and resid 601 through 606 removed outlier: 3.760A pdb=" N VAL G 605 " --> pdb=" O ASP G 601 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS G 606 " --> pdb=" O ALA G 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 606' Processing helix chain 'G' and resid 607 through 609 No H-bonds generated for 'chain 'G' and resid 607 through 609' Processing helix chain 'G' and resid 621 through 626 Processing helix chain 'G' and resid 699 through 704 removed outlier: 4.066A pdb=" N VAL G 703 " --> pdb=" O GLU G 699 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 713 Processing helix chain 'G' and resid 734 through 739 removed outlier: 3.768A pdb=" N VAL G 738 " --> pdb=" O LEU G 734 " (cutoff:3.500A) Processing helix chain 'G' and resid 740 through 742 No H-bonds generated for 'chain 'G' and resid 740 through 742' Processing helix chain 'G' and resid 747 through 751 Processing helix chain 'G' and resid 759 through 767 removed outlier: 4.078A pdb=" N ARG G 765 " --> pdb=" O GLU G 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 768 through 770 No H-bonds generated for 'chain 'G' and resid 768 through 770' Processing helix chain 'G' and resid 785 through 793 Processing helix chain 'G' and resid 813 through 816 removed outlier: 4.095A pdb=" N GLN G 816 " --> pdb=" O THR G 813 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 813 through 816' Processing helix chain 'G' and resid 817 through 829 Processing helix chain 'G' and resid 872 through 876 removed outlier: 3.727A pdb=" N ASN G 875 " --> pdb=" O THR G 872 " (cutoff:3.500A) Processing helix chain 'G' and resid 885 through 891 Processing helix chain 'G' and resid 906 through 911 Processing helix chain 'G' and resid 917 through 930 removed outlier: 4.049A pdb=" N ASP G 921 " --> pdb=" O VAL G 917 " (cutoff:3.500A) Processing helix chain 'G' and resid 931 through 943 removed outlier: 3.990A pdb=" N THR G 935 " --> pdb=" O ASP G 931 " (cutoff:3.500A) Processing helix chain 'G' and resid 946 through 957 removed outlier: 3.573A pdb=" N GLU G 956 " --> pdb=" O LEU G 952 " (cutoff:3.500A) Processing helix chain 'G' and resid 965 through 973 removed outlier: 3.564A pdb=" N ARG G 972 " --> pdb=" O THR G 968 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP G 973 " --> pdb=" O LEU G 969 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 992 Processing helix chain 'G' and resid 995 through 1007 removed outlier: 3.526A pdb=" N LEU G 999 " --> pdb=" O CYS G 995 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 164 Processing helix chain 'H' and resid 183 through 190 removed outlier: 4.483A pdb=" N LEU H 187 " --> pdb=" O ALA H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 209 through 219 Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'H' and resid 258 through 284 removed outlier: 4.111A pdb=" N VAL H 264 " --> pdb=" O ARG H 260 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR H 266 " --> pdb=" O LEU H 262 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N THR H 267 " --> pdb=" O ALA H 263 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY H 269 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Proline residue: H 270 - end of helix removed outlier: 3.723A pdb=" N GLY H 284 " --> pdb=" O CYS H 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402 removed outlier: 6.211A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 540 removed outlier: 4.121A pdb=" N LEU A 594 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.143A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.202A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU A 803 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS A 722 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 975 through 981 removed outlier: 4.262A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.542A pdb=" N ASP B 125 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 173 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 230 through 231 Processing sheet with id=AA9, first strand: chain 'C' and resid 139 through 140 Processing sheet with id=AB1, first strand: chain 'C' and resid 398 through 402 removed outlier: 3.633A pdb=" N HIS C 379 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 535 through 540 removed outlier: 4.117A pdb=" N LEU C 594 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.323A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 776 through 780 removed outlier: 3.643A pdb=" N GLY C 758 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL C 720 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU C 803 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS C 722 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 975 through 981 removed outlier: 4.306A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 102 through 103 removed outlier: 7.044A pdb=" N LEU D 102 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 124 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 203 through 204 removed outlier: 7.517A pdb=" N TRP D 203 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER D 240 " --> pdb=" O CYS D 231 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 139 through 140 Processing sheet with id=AB9, first strand: chain 'E' and resid 398 through 402 removed outlier: 3.539A pdb=" N HIS E 379 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY E 349 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N HIS E 344 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LEU E 423 " --> pdb=" O HIS E 344 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL E 346 " --> pdb=" O LEU E 423 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU E 425 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS E 348 " --> pdb=" O LEU E 425 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N CYS E 422 " --> pdb=" O ILE E 457 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLN E 459 " --> pdb=" O CYS E 422 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE E 424 " --> pdb=" O GLN E 459 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 535 through 540 removed outlier: 4.167A pdb=" N LEU E 594 " --> pdb=" O GLU E 569 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE E 598 " --> pdb=" O MET E 565 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N MET E 565 " --> pdb=" O ILE E 598 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 686 through 687 removed outlier: 4.241A pdb=" N TYR E 686 " --> pdb=" O GLY E 962 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 776 through 780 removed outlier: 6.315A pdb=" N ILE E 754 " --> pdb=" O SER E 777 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU E 779 " --> pdb=" O ILE E 754 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE E 756 " --> pdb=" O LEU E 779 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N CYS E 800 " --> pdb=" O ILE E 879 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLU E 881 " --> pdb=" O CYS E 800 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE E 802 " --> pdb=" O GLU E 881 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE E 915 " --> pdb=" O ILE E 878 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR E 880 " --> pdb=" O PHE E 915 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 975 through 981 removed outlier: 4.222A pdb=" N GLY E1013 " --> pdb=" O PHE E1050 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 99 through 100 removed outlier: 3.612A pdb=" N SER F 173 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 203 through 204 removed outlier: 6.449A pdb=" N TRP F 203 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 139 through 140 Processing sheet with id=AC8, first strand: chain 'G' and resid 398 through 402 removed outlier: 6.283A pdb=" N ILE G 345 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU G 378 " --> pdb=" O ILE G 345 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL G 347 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N HIS G 344 " --> pdb=" O ALA G 421 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU G 423 " --> pdb=" O HIS G 344 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL G 346 " --> pdb=" O LEU G 423 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU G 425 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N CYS G 348 " --> pdb=" O LEU G 425 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS G 422 " --> pdb=" O ILE G 457 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLN G 459 " --> pdb=" O CYS G 422 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE G 424 " --> pdb=" O GLN G 459 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 535 through 540 removed outlier: 6.859A pdb=" N LEU G 594 " --> pdb=" O ILE G 568 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE G 568 " --> pdb=" O LEU G 594 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE G 596 " --> pdb=" O ILE G 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 686 through 687 removed outlier: 4.145A pdb=" N TYR G 686 " --> pdb=" O GLY G 962 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 776 through 780 removed outlier: 6.447A pdb=" N ILE G 754 " --> pdb=" O SER G 777 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU G 779 " --> pdb=" O ILE G 754 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE G 756 " --> pdb=" O LEU G 779 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL G 720 " --> pdb=" O VAL G 801 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU G 803 " --> pdb=" O VAL G 720 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N CYS G 722 " --> pdb=" O LEU G 803 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 975 through 981 removed outlier: 3.949A pdb=" N GLY G1013 " --> pdb=" O PHE G1050 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU G1052 " --> pdb=" O CYS G1011 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS G1011 " --> pdb=" O LEU G1052 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 123 through 125 1469 hydrogen bonds defined for protein. 4113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.17 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6222 1.32 - 1.45: 9445 1.45 - 1.58: 20375 1.58 - 1.71: 2 1.71 - 1.83: 324 Bond restraints: 36368 Sorted by residual: bond pdb=" N LEU B 198 " pdb=" CA LEU B 198 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.27e-02 6.20e+03 1.34e+01 bond pdb=" N VAL B 50 " pdb=" CA VAL B 50 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.01e-02 9.80e+03 1.20e+01 bond pdb=" N CYS C 612 " pdb=" CA CYS C 612 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.12e+01 bond pdb=" N LEU F 60 " pdb=" CA LEU F 60 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" N VAL G 305 " pdb=" CA VAL G 305 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.17e-02 7.31e+03 1.04e+01 ... (remaining 36363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 48528 2.46 - 4.91: 781 4.91 - 7.37: 99 7.37 - 9.82: 9 9.82 - 12.28: 3 Bond angle restraints: 49420 Sorted by residual: angle pdb=" N ARG G 735 " pdb=" CA ARG G 735 " pdb=" C ARG G 735 " ideal model delta sigma weight residual 113.50 101.36 12.14 1.23e+00 6.61e-01 9.75e+01 angle pdb=" N LYS G 613 " pdb=" CA LYS G 613 " pdb=" C LYS G 613 " ideal model delta sigma weight residual 114.56 102.28 12.28 1.27e+00 6.20e-01 9.34e+01 angle pdb=" C ASN B 201 " pdb=" CA ASN B 201 " pdb=" CB ASN B 201 " ideal model delta sigma weight residual 109.45 100.93 8.52 1.45e+00 4.76e-01 3.45e+01 angle pdb=" N PRO B 202 " pdb=" CA PRO B 202 " pdb=" C PRO B 202 " ideal model delta sigma weight residual 112.33 102.44 9.89 1.87e+00 2.86e-01 2.80e+01 angle pdb=" CA VAL G 293 " pdb=" C VAL G 293 " pdb=" O VAL G 293 " ideal model delta sigma weight residual 121.75 115.69 6.06 1.18e+00 7.18e-01 2.63e+01 ... (remaining 49415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19714 17.96 - 35.93: 1563 35.93 - 53.89: 310 53.89 - 71.86: 45 71.86 - 89.82: 20 Dihedral angle restraints: 21652 sinusoidal: 8428 harmonic: 13224 Sorted by residual: dihedral pdb=" CB CYS B 47 " pdb=" SG CYS B 47 " pdb=" SG CYS B 57 " pdb=" CB CYS B 57 " ideal model delta sinusoidal sigma weight residual 93.00 14.92 78.08 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB CYS F 47 " pdb=" SG CYS F 47 " pdb=" SG CYS F 57 " pdb=" CB CYS F 57 " ideal model delta sinusoidal sigma weight residual -86.00 -128.27 42.27 1 1.00e+01 1.00e-02 2.50e+01 dihedral pdb=" CA VAL A 319 " pdb=" C VAL A 319 " pdb=" N PRO A 320 " pdb=" CA PRO A 320 " ideal model delta harmonic sigma weight residual -180.00 -156.08 -23.92 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 21649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 5073 0.070 - 0.141: 541 0.141 - 0.211: 62 0.211 - 0.282: 23 0.282 - 0.352: 5 Chirality restraints: 5704 Sorted by residual: chirality pdb=" CA ALA F 59 " pdb=" N ALA F 59 " pdb=" C ALA F 59 " pdb=" CB ALA F 59 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA THR C 942 " pdb=" N THR C 942 " pdb=" C THR C 942 " pdb=" CB THR C 942 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA CYS E 612 " pdb=" N CYS E 612 " pdb=" C CYS E 612 " pdb=" CB CYS E 612 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 5701 not shown) Planarity restraints: 6264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 610 " 0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C PHE G 610 " -0.077 2.00e-02 2.50e+03 pdb=" O PHE G 610 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR G 611 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 946 " -0.067 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO E 947 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO E 947 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 947 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 985 " -0.061 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO C 986 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.049 5.00e-02 4.00e+02 ... (remaining 6261 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 450 2.66 - 3.22: 34356 3.22 - 3.78: 55557 3.78 - 4.34: 76561 4.34 - 4.90: 124074 Nonbonded interactions: 290998 Sorted by model distance: nonbonded pdb=" ND2 ASN G 895 " pdb=" NE2 GLN G 907 " model vdw 2.097 3.200 nonbonded pdb=" OH TYR A 290 " pdb=" CE MET G 304 " model vdw 2.151 3.460 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR E 290 " model vdw 2.200 3.040 nonbonded pdb=" OG SER E 600 " pdb=" OE2 GLU E 604 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP E 811 " pdb=" NZ LYS E 818 " model vdw 2.232 3.120 ... (remaining 290993 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.350 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 36376 Z= 0.240 Angle : 0.723 12.277 49436 Z= 0.436 Chirality : 0.048 0.352 5704 Planarity : 0.005 0.100 6264 Dihedral : 13.556 89.823 13060 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.44 % Allowed : 0.83 % Favored : 98.74 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 4504 helix: 0.77 (0.12), residues: 1840 sheet: -1.13 (0.21), residues: 576 loop : -0.48 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 393 TYR 0.027 0.002 TYR A1015 PHE 0.026 0.002 PHE G 307 TRP 0.020 0.002 TRP A 203 HIS 0.007 0.001 HIS E 616 Details of bonding type rmsd covalent geometry : bond 0.00391 (36368) covalent geometry : angle 0.72089 (49420) SS BOND : bond 0.00750 ( 8) SS BOND : angle 3.06633 ( 16) hydrogen bonds : bond 0.15847 ( 1469) hydrogen bonds : angle 6.29155 ( 4113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 624 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.6714 (m-10) cc_final: 0.6460 (m-10) REVERT: E 309 LEU cc_start: 0.8523 (mt) cc_final: 0.8289 (mt) outliers start: 17 outliers final: 1 residues processed: 635 average time/residue: 0.2049 time to fit residues: 216.4893 Evaluate side-chains 354 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 290 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 50.0000 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 907 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 HIS E 753 HIS ** E 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 ASN G 465 ASN G 468 HIS ** G 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 884 ASN G 887 ASN H 80 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.051712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035326 restraints weight = 237162.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.036385 restraints weight = 142049.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037094 restraints weight = 98940.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.037636 restraints weight = 76619.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.037984 restraints weight = 62999.711| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36376 Z= 0.193 Angle : 0.681 11.755 49436 Z= 0.337 Chirality : 0.043 0.255 5704 Planarity : 0.005 0.070 6264 Dihedral : 4.356 37.363 4874 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.44 % Allowed : 10.11 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.12), residues: 4504 helix: 0.74 (0.12), residues: 1928 sheet: -0.93 (0.21), residues: 572 loop : -0.50 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 974 TYR 0.026 0.002 TYR A 318 PHE 0.041 0.002 PHE G 307 TRP 0.015 0.001 TRP C 100 HIS 0.010 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00411 (36368) covalent geometry : angle 0.68034 (49420) SS BOND : bond 0.01446 ( 8) SS BOND : angle 2.14019 ( 16) hydrogen bonds : bond 0.04160 ( 1469) hydrogen bonds : angle 5.32332 ( 4113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 370 time to evaluate : 1.041 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 215 ILE cc_start: 0.9363 (mt) cc_final: 0.9150 (mm) REVERT: A 460 MET cc_start: 0.8897 (tpp) cc_final: 0.8581 (mmm) REVERT: A 691 MET cc_start: 0.9341 (mmp) cc_final: 0.9082 (mmm) REVERT: A 1009 MET cc_start: 0.8452 (mmm) cc_final: 0.7632 (mmm) REVERT: A 1053 MET cc_start: 0.8602 (mmm) cc_final: 0.8332 (mmm) REVERT: C 30 MET cc_start: 0.8720 (ppp) cc_final: 0.8515 (ppp) REVERT: C 104 MET cc_start: 0.9163 (mmp) cc_final: 0.8871 (mmm) REVERT: C 272 LEU cc_start: 0.8778 (mt) cc_final: 0.8516 (mt) REVERT: C 460 MET cc_start: 0.9082 (tpp) cc_final: 0.8867 (tpp) REVERT: C 506 MET cc_start: 0.9318 (mmt) cc_final: 0.9053 (mmt) REVERT: C 565 MET cc_start: 0.9261 (tpt) cc_final: 0.9042 (tpp) REVERT: C 830 MET cc_start: 0.9016 (mmm) cc_final: 0.8545 (mmt) REVERT: C 1009 MET cc_start: 0.8665 (mmp) cc_final: 0.8294 (mmp) REVERT: D 273 PHE cc_start: 0.9177 (m-80) cc_final: 0.8807 (m-80) REVERT: D 277 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8618 (tt) REVERT: E 21 MET cc_start: 0.8672 (mmm) cc_final: 0.8340 (mmm) REVERT: E 194 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.9085 (m-80) REVERT: E 213 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8768 (mmm160) REVERT: E 303 PHE cc_start: 0.9438 (m-80) cc_final: 0.8912 (t80) REVERT: E 314 MET cc_start: 0.8623 (tmm) cc_final: 0.8347 (tmm) REVERT: E 318 TYR cc_start: 0.8661 (t80) cc_final: 0.8335 (t80) REVERT: E 388 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8991 (mp0) REVERT: E 442 MET cc_start: 0.9645 (ttp) cc_final: 0.9350 (mtm) REVERT: E 513 MET cc_start: 0.7677 (ttp) cc_final: 0.7121 (ttp) REVERT: E 565 MET cc_start: 0.8571 (tpp) cc_final: 0.7404 (tpp) REVERT: E 691 MET cc_start: 0.9644 (mmm) cc_final: 0.8862 (tpp) REVERT: E 799 MET cc_start: 0.9583 (tpp) cc_final: 0.9272 (tpp) REVERT: E 830 MET cc_start: 0.8794 (tpp) cc_final: 0.8590 (mmm) REVERT: F 172 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9091 (mp) REVERT: F 273 PHE cc_start: 0.9053 (m-80) cc_final: 0.8726 (m-80) REVERT: G 118 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9501 (pp) REVERT: G 194 PHE cc_start: 0.8566 (m-80) cc_final: 0.8303 (m-80) REVERT: G 734 LEU cc_start: 0.9729 (mt) cc_final: 0.9330 (mp) REVERT: G 830 MET cc_start: 0.8962 (mmt) cc_final: 0.8567 (mmt) REVERT: G 1009 MET cc_start: 0.8282 (mmp) cc_final: 0.7775 (mmp) outliers start: 56 outliers final: 23 residues processed: 403 average time/residue: 0.1947 time to fit residues: 134.0450 Evaluate side-chains 340 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 312 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 1012 PHE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 1012 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 143 optimal weight: 1.9990 chunk 421 optimal weight: 0.2980 chunk 32 optimal weight: 6.9990 chunk 347 optimal weight: 9.9990 chunk 360 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 350 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 HIS ** E 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 464 HIS ** G 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 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 = 0.3302 r_free = 0.3302 target = 0.051304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.034931 restraints weight = 236566.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.035994 restraints weight = 140641.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.036727 restraints weight = 97728.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.037259 restraints weight = 75070.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037601 restraints weight = 61751.859| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36376 Z= 0.143 Angle : 0.617 11.053 49436 Z= 0.304 Chirality : 0.041 0.339 5704 Planarity : 0.005 0.067 6264 Dihedral : 4.231 26.285 4872 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.26 % Allowed : 12.72 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 4504 helix: 1.03 (0.12), residues: 1868 sheet: -0.62 (0.23), residues: 532 loop : -0.32 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 974 TYR 0.015 0.001 TYR A1015 PHE 0.043 0.002 PHE G 223 TRP 0.013 0.001 TRP G 477 HIS 0.006 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00311 (36368) covalent geometry : angle 0.61580 (49420) SS BOND : bond 0.00414 ( 8) SS BOND : angle 2.17751 ( 16) hydrogen bonds : bond 0.03697 ( 1469) hydrogen bonds : angle 5.08033 ( 4113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 331 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 MET cc_start: 0.9271 (mmp) cc_final: 0.8990 (mmm) REVERT: A 830 MET cc_start: 0.8974 (mmt) cc_final: 0.8534 (mmm) REVERT: C 104 MET cc_start: 0.9132 (mmp) cc_final: 0.8816 (mmp) REVERT: C 506 MET cc_start: 0.9272 (mmt) cc_final: 0.8999 (mmt) REVERT: C 565 MET cc_start: 0.9265 (tpt) cc_final: 0.8974 (tpp) REVERT: C 691 MET cc_start: 0.9338 (mmm) cc_final: 0.8919 (tpp) REVERT: C 830 MET cc_start: 0.9065 (mmm) cc_final: 0.8559 (mmt) REVERT: C 891 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9313 (mm) REVERT: D 273 PHE cc_start: 0.9229 (m-80) cc_final: 0.8840 (m-80) REVERT: D 277 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8593 (tt) REVERT: E 194 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.9080 (m-80) REVERT: E 213 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8700 (mmm160) REVERT: E 252 PHE cc_start: 0.9474 (t80) cc_final: 0.9075 (t80) REVERT: E 303 PHE cc_start: 0.9389 (m-80) cc_final: 0.8746 (t80) REVERT: E 314 MET cc_start: 0.8572 (tmm) cc_final: 0.8308 (tmm) REVERT: E 318 TYR cc_start: 0.8764 (t80) cc_final: 0.8340 (t80) REVERT: E 388 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9025 (mp0) REVERT: E 442 MET cc_start: 0.9637 (ttp) cc_final: 0.9384 (mtm) REVERT: E 513 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7295 (ttp) REVERT: E 691 MET cc_start: 0.9660 (mmm) cc_final: 0.8894 (tpp) REVERT: E 799 MET cc_start: 0.9567 (tpp) cc_final: 0.9272 (tpp) REVERT: F 172 LEU cc_start: 0.9637 (tp) cc_final: 0.9242 (mm) REVERT: F 273 PHE cc_start: 0.9092 (m-80) cc_final: 0.8529 (m-80) REVERT: G 153 ASP cc_start: 0.9329 (t0) cc_final: 0.8811 (t0) REVERT: G 194 PHE cc_start: 0.8591 (m-80) cc_final: 0.8349 (m-80) REVERT: G 285 MET cc_start: 0.9281 (mmm) cc_final: 0.8960 (mmm) REVERT: G 734 LEU cc_start: 0.9742 (mt) cc_final: 0.9377 (mp) REVERT: G 1049 ILE cc_start: 0.9681 (mt) cc_final: 0.9358 (tp) REVERT: G 1053 MET cc_start: 0.8726 (mmm) cc_final: 0.8519 (mmm) outliers start: 49 outliers final: 17 residues processed: 367 average time/residue: 0.1898 time to fit residues: 119.5377 Evaluate side-chains 333 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 311 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 555 GLU Chi-restraints excluded: chain E residue 1012 PHE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 1012 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 408 optimal weight: 10.0000 chunk 360 optimal weight: 8.9990 chunk 226 optimal weight: 20.0000 chunk 380 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 284 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 446 optimal weight: 9.9990 chunk 210 optimal weight: 40.0000 chunk 233 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS A 957 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN ** G 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 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 = 0.3290 r_free = 0.3290 target = 0.050544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.034332 restraints weight = 239448.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035354 restraints weight = 144121.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.036095 restraints weight = 100490.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.036615 restraints weight = 77611.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.036969 restraints weight = 63689.461| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36376 Z= 0.172 Angle : 0.609 11.021 49436 Z= 0.300 Chirality : 0.041 0.293 5704 Planarity : 0.004 0.067 6264 Dihedral : 4.167 25.729 4872 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.70 % Allowed : 13.93 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.13), residues: 4504 helix: 1.14 (0.12), residues: 1876 sheet: -0.53 (0.23), residues: 528 loop : -0.25 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 960 TYR 0.019 0.002 TYR A 198 PHE 0.041 0.002 PHE A 223 TRP 0.015 0.001 TRP G 477 HIS 0.005 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00366 (36368) covalent geometry : angle 0.60836 (49420) SS BOND : bond 0.00277 ( 8) SS BOND : angle 1.64619 ( 16) hydrogen bonds : bond 0.03487 ( 1469) hydrogen bonds : angle 4.99269 ( 4113) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 323 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8610 (mmt) cc_final: 0.8343 (mpp) REVERT: A 186 ASP cc_start: 0.9543 (m-30) cc_final: 0.9086 (m-30) REVERT: A 252 PHE cc_start: 0.9584 (OUTLIER) cc_final: 0.9222 (t80) REVERT: A 576 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8057 (tp30) REVERT: A 763 LEU cc_start: 0.9875 (OUTLIER) cc_final: 0.9636 (mt) REVERT: A 830 MET cc_start: 0.9020 (mmt) cc_final: 0.8611 (mmm) REVERT: A 1009 MET cc_start: 0.8569 (mmm) cc_final: 0.8130 (mmm) REVERT: C 104 MET cc_start: 0.9181 (mmp) cc_final: 0.8957 (mmm) REVERT: C 506 MET cc_start: 0.9320 (mmt) cc_final: 0.8967 (mmt) REVERT: C 510 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9253 (mm) REVERT: C 565 MET cc_start: 0.9308 (tpt) cc_final: 0.8948 (tpp) REVERT: C 691 MET cc_start: 0.9465 (mmm) cc_final: 0.9090 (tpp) REVERT: C 830 MET cc_start: 0.9108 (mmm) cc_final: 0.8587 (mmt) REVERT: C 891 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9333 (mm) REVERT: D 273 PHE cc_start: 0.9290 (m-80) cc_final: 0.8917 (m-80) REVERT: D 277 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8673 (tt) REVERT: E 194 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.9099 (m-80) REVERT: E 213 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8832 (mmm-85) REVERT: E 252 PHE cc_start: 0.9415 (t80) cc_final: 0.9109 (t80) REVERT: E 303 PHE cc_start: 0.9392 (m-80) cc_final: 0.8789 (t80) REVERT: E 318 TYR cc_start: 0.8840 (t80) cc_final: 0.8431 (t80) REVERT: E 388 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9027 (mp0) REVERT: E 442 MET cc_start: 0.9633 (ttp) cc_final: 0.9373 (mtm) REVERT: E 513 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7333 (ttp) REVERT: E 691 MET cc_start: 0.9669 (mmm) cc_final: 0.9422 (tpp) REVERT: E 799 MET cc_start: 0.9559 (tpp) cc_final: 0.9300 (tpp) REVERT: E 830 MET cc_start: 0.8835 (mmm) cc_final: 0.8586 (mmm) REVERT: F 273 PHE cc_start: 0.9099 (m-80) cc_final: 0.8495 (m-80) REVERT: G 153 ASP cc_start: 0.9344 (t0) cc_final: 0.8953 (t0) REVERT: G 194 PHE cc_start: 0.8680 (m-80) cc_final: 0.8457 (m-80) REVERT: G 285 MET cc_start: 0.9325 (mmm) cc_final: 0.8945 (mmm) REVERT: G 318 TYR cc_start: 0.8972 (t80) cc_final: 0.8473 (t80) REVERT: G 442 MET cc_start: 0.9579 (ttp) cc_final: 0.9210 (mtm) REVERT: G 460 MET cc_start: 0.9081 (mtp) cc_final: 0.8612 (ttt) REVERT: G 734 LEU cc_start: 0.9782 (mt) cc_final: 0.9388 (mp) REVERT: G 885 ASP cc_start: 0.9161 (p0) cc_final: 0.8950 (p0) REVERT: G 1049 ILE cc_start: 0.9701 (mt) cc_final: 0.9383 (tp) outliers start: 66 outliers final: 35 residues processed: 369 average time/residue: 0.1887 time to fit residues: 119.9865 Evaluate side-chains 344 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 754 ILE Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 555 GLU Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain E residue 1012 PHE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 1012 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 285 optimal weight: 0.9980 chunk 210 optimal weight: 50.0000 chunk 279 optimal weight: 8.9990 chunk 292 optimal weight: 3.9990 chunk 355 optimal weight: 2.9990 chunk 237 optimal weight: 0.0370 chunk 151 optimal weight: 5.9990 chunk 223 optimal weight: 20.0000 chunk 263 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 275 optimal weight: 10.0000 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN C 586 HIS ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.051489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.035179 restraints weight = 234219.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.036229 restraints weight = 139564.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.036973 restraints weight = 96909.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.037460 restraints weight = 74825.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.037839 restraints weight = 62000.134| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 36376 Z= 0.105 Angle : 0.602 11.435 49436 Z= 0.288 Chirality : 0.040 0.219 5704 Planarity : 0.004 0.063 6264 Dihedral : 4.067 25.796 4872 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.44 % Allowed : 15.51 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 4504 helix: 1.14 (0.12), residues: 1892 sheet: -0.45 (0.23), residues: 528 loop : -0.25 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 143 TYR 0.040 0.001 TYR A 163 PHE 0.029 0.001 PHE G 223 TRP 0.018 0.001 TRP G 477 HIS 0.007 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00234 (36368) covalent geometry : angle 0.60203 (49420) SS BOND : bond 0.00861 ( 8) SS BOND : angle 1.28448 ( 16) hydrogen bonds : bond 0.03324 ( 1469) hydrogen bonds : angle 4.80199 ( 4113) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 331 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASP cc_start: 0.9492 (m-30) cc_final: 0.9028 (m-30) REVERT: A 252 PHE cc_start: 0.9595 (OUTLIER) cc_final: 0.9102 (t80) REVERT: A 691 MET cc_start: 0.9526 (tpp) cc_final: 0.8685 (mmm) REVERT: A 830 MET cc_start: 0.9076 (mmt) cc_final: 0.8598 (mmm) REVERT: C 506 MET cc_start: 0.9297 (mmt) cc_final: 0.8911 (mmt) REVERT: C 510 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9293 (mm) REVERT: C 565 MET cc_start: 0.9370 (tpt) cc_final: 0.8981 (tpp) REVERT: C 691 MET cc_start: 0.9495 (mmm) cc_final: 0.9134 (tpp) REVERT: C 830 MET cc_start: 0.9111 (mmm) cc_final: 0.8594 (mmt) REVERT: C 891 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9274 (mm) REVERT: D 273 PHE cc_start: 0.9303 (m-80) cc_final: 0.8927 (m-80) REVERT: D 277 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8672 (tt) REVERT: E 194 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.9053 (m-80) REVERT: E 213 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8125 (mmm160) REVERT: E 252 PHE cc_start: 0.9404 (t80) cc_final: 0.8876 (t80) REVERT: E 303 PHE cc_start: 0.9367 (m-80) cc_final: 0.8666 (t80) REVERT: E 314 MET cc_start: 0.8618 (tmm) cc_final: 0.8202 (tmm) REVERT: E 318 TYR cc_start: 0.8758 (t80) cc_final: 0.8327 (t80) REVERT: E 388 GLU cc_start: 0.9341 (mt-10) cc_final: 0.9032 (mp0) REVERT: E 442 MET cc_start: 0.9619 (ttp) cc_final: 0.9374 (mtm) REVERT: E 513 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7401 (ttp) REVERT: E 691 MET cc_start: 0.9638 (mmm) cc_final: 0.8828 (tpp) REVERT: E 799 MET cc_start: 0.9555 (tpp) cc_final: 0.9297 (tpp) REVERT: E 830 MET cc_start: 0.8872 (mmm) cc_final: 0.8589 (mmm) REVERT: F 273 PHE cc_start: 0.9099 (m-80) cc_final: 0.8444 (m-80) REVERT: G 118 LEU cc_start: 0.9723 (mm) cc_final: 0.9500 (pp) REVERT: G 153 ASP cc_start: 0.9340 (t0) cc_final: 0.8830 (t0) REVERT: G 318 TYR cc_start: 0.8929 (t80) cc_final: 0.8405 (t80) REVERT: G 442 MET cc_start: 0.9581 (ttp) cc_final: 0.9185 (mtm) REVERT: G 460 MET cc_start: 0.9085 (mtp) cc_final: 0.8748 (tpp) REVERT: G 565 MET cc_start: 0.8901 (tpt) cc_final: 0.8688 (tpt) REVERT: G 734 LEU cc_start: 0.9782 (mt) cc_final: 0.9403 (mp) REVERT: G 885 ASP cc_start: 0.9133 (p0) cc_final: 0.8871 (p0) REVERT: G 1049 ILE cc_start: 0.9720 (mt) cc_final: 0.9417 (tp) REVERT: G 1053 MET cc_start: 0.8726 (mmm) cc_final: 0.8495 (mmm) outliers start: 56 outliers final: 28 residues processed: 372 average time/residue: 0.1861 time to fit residues: 120.3225 Evaluate side-chains 337 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 302 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 555 GLU Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain E residue 946 THR Chi-restraints excluded: chain E residue 1012 PHE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 1012 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 380 optimal weight: 3.9990 chunk 435 optimal weight: 6.9990 chunk 451 optimal weight: 8.9990 chunk 333 optimal weight: 50.0000 chunk 366 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 351 optimal weight: 6.9990 chunk 54 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 793 ASN ** E 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 753 HIS ** G 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.049733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.033648 restraints weight = 244474.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.034644 restraints weight = 146207.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.035340 restraints weight = 102207.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.035832 restraints weight = 79096.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.036156 restraints weight = 65495.513| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36376 Z= 0.196 Angle : 0.632 11.757 49436 Z= 0.307 Chirality : 0.040 0.322 5704 Planarity : 0.004 0.068 6264 Dihedral : 4.094 26.361 4872 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.06 % Allowed : 16.20 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4504 helix: 1.15 (0.12), residues: 1888 sheet: -0.41 (0.23), residues: 524 loop : -0.21 (0.14), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 960 TYR 0.015 0.001 TYR A 429 PHE 0.032 0.002 PHE G 223 TRP 0.016 0.001 TRP A 178 HIS 0.006 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00414 (36368) covalent geometry : angle 0.63145 (49420) SS BOND : bond 0.00237 ( 8) SS BOND : angle 1.17866 ( 16) hydrogen bonds : bond 0.03398 ( 1469) hydrogen bonds : angle 4.93094 ( 4113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 296 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8621 (mmt) cc_final: 0.8410 (mpp) REVERT: A 186 ASP cc_start: 0.9536 (m-30) cc_final: 0.9039 (m-30) REVERT: A 252 PHE cc_start: 0.9566 (OUTLIER) cc_final: 0.9010 (t80) REVERT: A 303 PHE cc_start: 0.9477 (m-80) cc_final: 0.8910 (t80) REVERT: A 460 MET cc_start: 0.8992 (tpp) cc_final: 0.8578 (tpp) REVERT: A 565 MET cc_start: 0.8219 (tpp) cc_final: 0.8002 (tpt) REVERT: A 763 LEU cc_start: 0.9884 (OUTLIER) cc_final: 0.9644 (mt) REVERT: C 104 MET cc_start: 0.9024 (mmm) cc_final: 0.8754 (mmm) REVERT: C 506 MET cc_start: 0.9290 (mmt) cc_final: 0.8924 (mmt) REVERT: C 510 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9311 (mm) REVERT: C 565 MET cc_start: 0.9341 (tpt) cc_final: 0.8938 (tpp) REVERT: C 691 MET cc_start: 0.9528 (mmm) cc_final: 0.9170 (tpp) REVERT: C 739 MET cc_start: 0.9605 (mtp) cc_final: 0.9287 (mtm) REVERT: C 830 MET cc_start: 0.9017 (mmm) cc_final: 0.8500 (mmt) REVERT: C 891 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9371 (mm) REVERT: C 1053 MET cc_start: 0.9120 (mtp) cc_final: 0.8827 (mmm) REVERT: D 194 ASP cc_start: 0.9134 (p0) cc_final: 0.8910 (p0) REVERT: D 273 PHE cc_start: 0.9357 (m-80) cc_final: 0.8949 (m-80) REVERT: E 154 MET cc_start: 0.9586 (tpt) cc_final: 0.9350 (tpt) REVERT: E 194 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.9002 (m-80) REVERT: E 213 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8316 (mmm160) REVERT: E 221 LEU cc_start: 0.9850 (OUTLIER) cc_final: 0.9648 (tp) REVERT: E 223 PHE cc_start: 0.9028 (m-80) cc_final: 0.8824 (m-80) REVERT: E 252 PHE cc_start: 0.9384 (t80) cc_final: 0.9022 (t80) REVERT: E 303 PHE cc_start: 0.9407 (m-80) cc_final: 0.8808 (t80) REVERT: E 318 TYR cc_start: 0.8939 (t80) cc_final: 0.8455 (t80) REVERT: E 442 MET cc_start: 0.9655 (ttp) cc_final: 0.9385 (mtm) REVERT: E 513 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7406 (ttp) REVERT: E 691 MET cc_start: 0.9663 (mmm) cc_final: 0.9452 (tpp) REVERT: E 799 MET cc_start: 0.9557 (tpp) cc_final: 0.9327 (tpp) REVERT: F 273 PHE cc_start: 0.9155 (m-80) cc_final: 0.8474 (m-80) REVERT: G 118 LEU cc_start: 0.9726 (mm) cc_final: 0.9510 (pp) REVERT: G 153 ASP cc_start: 0.9394 (t0) cc_final: 0.8905 (t0) REVERT: G 223 PHE cc_start: 0.8125 (m-80) cc_final: 0.7906 (m-80) REVERT: G 318 TYR cc_start: 0.9001 (t80) cc_final: 0.8515 (t80) REVERT: G 460 MET cc_start: 0.9124 (mtp) cc_final: 0.8814 (tpp) REVERT: G 885 ASP cc_start: 0.9182 (p0) cc_final: 0.8874 (p0) REVERT: G 1009 MET cc_start: 0.8128 (mmm) cc_final: 0.7308 (mmm) REVERT: G 1049 ILE cc_start: 0.9712 (mt) cc_final: 0.9376 (tp) outliers start: 80 outliers final: 43 residues processed: 354 average time/residue: 0.1870 time to fit residues: 114.6911 Evaluate side-chains 341 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 555 GLU Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain E residue 946 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 1012 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 145 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 163 optimal weight: 0.0770 chunk 310 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 93 optimal weight: 50.0000 chunk 42 optimal weight: 2.9990 overall best weight: 1.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 GLN ** G 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** 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 = 0.3300 r_free = 0.3300 target = 0.050636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.034481 restraints weight = 237305.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.035511 restraints weight = 141270.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.036237 restraints weight = 98309.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.036740 restraints weight = 75826.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037065 restraints weight = 62679.244| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 36376 Z= 0.110 Angle : 0.619 13.993 49436 Z= 0.293 Chirality : 0.041 0.350 5704 Planarity : 0.004 0.066 6264 Dihedral : 4.034 25.474 4872 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.60 % Allowed : 17.21 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.13), residues: 4504 helix: 1.16 (0.12), residues: 1904 sheet: -0.38 (0.23), residues: 524 loop : -0.19 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 157 TYR 0.019 0.001 TYR G 318 PHE 0.025 0.001 PHE G 511 TRP 0.017 0.001 TRP A 178 HIS 0.006 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00246 (36368) covalent geometry : angle 0.61927 (49420) SS BOND : bond 0.00192 ( 8) SS BOND : angle 0.99680 ( 16) hydrogen bonds : bond 0.03240 ( 1469) hydrogen bonds : angle 4.75268 ( 4113) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 316 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASP cc_start: 0.9496 (m-30) cc_final: 0.9012 (m-30) REVERT: A 252 PHE cc_start: 0.9576 (OUTLIER) cc_final: 0.8975 (t80) REVERT: A 303 PHE cc_start: 0.9487 (m-80) cc_final: 0.8868 (t80) REVERT: A 352 THR cc_start: 0.9574 (OUTLIER) cc_final: 0.9266 (p) REVERT: A 440 ASN cc_start: 0.9773 (m-40) cc_final: 0.9510 (m110) REVERT: A 442 MET cc_start: 0.9581 (ttp) cc_final: 0.9263 (mtm) REVERT: A 565 MET cc_start: 0.8192 (tpp) cc_final: 0.7967 (tpt) REVERT: A 763 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9611 (mt) REVERT: A 830 MET cc_start: 0.9103 (mmt) cc_final: 0.8592 (mmm) REVERT: C 104 MET cc_start: 0.8988 (mmm) cc_final: 0.8727 (mmm) REVERT: C 506 MET cc_start: 0.9283 (mmt) cc_final: 0.8891 (mmt) REVERT: C 510 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9279 (mm) REVERT: C 565 MET cc_start: 0.9345 (tpt) cc_final: 0.9070 (tpp) REVERT: C 691 MET cc_start: 0.9492 (mmm) cc_final: 0.9171 (tpp) REVERT: C 739 MET cc_start: 0.9611 (mtp) cc_final: 0.9281 (mtm) REVERT: C 830 MET cc_start: 0.9047 (mmm) cc_final: 0.8512 (mmt) REVERT: C 891 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9327 (mm) REVERT: D 194 ASP cc_start: 0.9051 (p0) cc_final: 0.8834 (p0) REVERT: D 273 PHE cc_start: 0.9351 (m-80) cc_final: 0.8933 (m-80) REVERT: D 277 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8772 (tt) REVERT: E 194 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.9000 (m-80) REVERT: E 213 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8240 (mmm160) REVERT: E 223 PHE cc_start: 0.8970 (m-80) cc_final: 0.8707 (m-80) REVERT: E 252 PHE cc_start: 0.9400 (t80) cc_final: 0.9000 (t80) REVERT: E 303 PHE cc_start: 0.9367 (m-80) cc_final: 0.8759 (t80) REVERT: E 314 MET cc_start: 0.8600 (tmm) cc_final: 0.8384 (ppp) REVERT: E 318 TYR cc_start: 0.8940 (t80) cc_final: 0.8481 (t80) REVERT: E 388 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9032 (mp0) REVERT: E 442 MET cc_start: 0.9615 (ttp) cc_final: 0.9364 (mtm) REVERT: E 513 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7423 (ttp) REVERT: E 597 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: E 799 MET cc_start: 0.9535 (tpp) cc_final: 0.9309 (tpp) REVERT: F 172 LEU cc_start: 0.9684 (tp) cc_final: 0.9262 (mm) REVERT: F 273 PHE cc_start: 0.9126 (m-80) cc_final: 0.8433 (m-80) REVERT: G 118 LEU cc_start: 0.9706 (mm) cc_final: 0.9344 (pp) REVERT: G 153 ASP cc_start: 0.9406 (t0) cc_final: 0.9023 (t0) REVERT: G 281 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9440 (tp) REVERT: G 285 MET cc_start: 0.9313 (mmt) cc_final: 0.8812 (mmm) REVERT: G 318 TYR cc_start: 0.9006 (t80) cc_final: 0.8509 (t80) REVERT: G 442 MET cc_start: 0.9586 (ttp) cc_final: 0.9181 (mtm) REVERT: G 460 MET cc_start: 0.9093 (mtp) cc_final: 0.8841 (tpp) REVERT: G 503 LEU cc_start: 0.9676 (tp) cc_final: 0.9391 (tp) REVERT: G 885 ASP cc_start: 0.9163 (p0) cc_final: 0.8859 (p0) REVERT: G 1009 MET cc_start: 0.8001 (mmm) cc_final: 0.7385 (mmm) REVERT: G 1049 ILE cc_start: 0.9707 (mt) cc_final: 0.9396 (tp) outliers start: 62 outliers final: 34 residues processed: 361 average time/residue: 0.1829 time to fit residues: 116.6561 Evaluate side-chains 337 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 555 GLU Chi-restraints excluded: chain E residue 597 PHE Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain E residue 946 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 1012 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 289 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 447 optimal weight: 8.9990 chunk 428 optimal weight: 4.9990 chunk 276 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 353 optimal weight: 9.9990 chunk 319 optimal weight: 9.9990 chunk 398 optimal weight: 10.0000 chunk 409 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN ** E 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.050004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.033945 restraints weight = 239588.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.034947 restraints weight = 143242.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.035657 restraints weight = 99937.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036130 restraints weight = 77350.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.036489 restraints weight = 64210.204| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36376 Z= 0.140 Angle : 0.633 13.441 49436 Z= 0.300 Chirality : 0.040 0.356 5704 Planarity : 0.004 0.066 6264 Dihedral : 4.009 25.545 4872 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.60 % Allowed : 17.91 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.13), residues: 4504 helix: 1.16 (0.12), residues: 1904 sheet: -0.38 (0.24), residues: 524 loop : -0.16 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 157 TYR 0.027 0.001 TYR G 274 PHE 0.046 0.001 PHE G 223 TRP 0.017 0.001 TRP A 178 HIS 0.005 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00308 (36368) covalent geometry : angle 0.63236 (49420) SS BOND : bond 0.00201 ( 8) SS BOND : angle 1.05964 ( 16) hydrogen bonds : bond 0.03262 ( 1469) hydrogen bonds : angle 4.79094 ( 4113) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASP cc_start: 0.9504 (m-30) cc_final: 0.8999 (m-30) REVERT: A 252 PHE cc_start: 0.9583 (OUTLIER) cc_final: 0.8943 (t80) REVERT: A 303 PHE cc_start: 0.9492 (m-80) cc_final: 0.8821 (t80) REVERT: A 352 THR cc_start: 0.9564 (OUTLIER) cc_final: 0.9260 (p) REVERT: A 442 MET cc_start: 0.9609 (ttp) cc_final: 0.9200 (mtm) REVERT: A 460 MET cc_start: 0.8983 (tpp) cc_final: 0.8687 (tpp) REVERT: A 763 LEU cc_start: 0.9862 (OUTLIER) cc_final: 0.9630 (mt) REVERT: A 830 MET cc_start: 0.9151 (mmt) cc_final: 0.8634 (mmm) REVERT: A 881 GLU cc_start: 0.9072 (tt0) cc_final: 0.8754 (tt0) REVERT: A 1009 MET cc_start: 0.8868 (mmm) cc_final: 0.8305 (mmm) REVERT: B 203 TRP cc_start: 0.8330 (t60) cc_final: 0.7801 (t-100) REVERT: C 104 MET cc_start: 0.8961 (mmm) cc_final: 0.8753 (mmm) REVERT: C 506 MET cc_start: 0.9291 (mmt) cc_final: 0.8891 (mmt) REVERT: C 510 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9309 (mm) REVERT: C 565 MET cc_start: 0.9361 (tpt) cc_final: 0.8873 (tpp) REVERT: C 691 MET cc_start: 0.9483 (mmm) cc_final: 0.9201 (tpp) REVERT: C 739 MET cc_start: 0.9615 (mtp) cc_final: 0.9279 (mtm) REVERT: C 830 MET cc_start: 0.9046 (mmm) cc_final: 0.8516 (mmt) REVERT: C 891 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9338 (mm) REVERT: D 194 ASP cc_start: 0.9014 (p0) cc_final: 0.8805 (p0) REVERT: D 273 PHE cc_start: 0.9363 (m-80) cc_final: 0.8954 (m-80) REVERT: D 277 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8812 (tt) REVERT: E 194 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8978 (m-80) REVERT: E 213 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8161 (mmm160) REVERT: E 223 PHE cc_start: 0.8948 (m-80) cc_final: 0.8587 (m-80) REVERT: E 252 PHE cc_start: 0.9380 (t80) cc_final: 0.8986 (t80) REVERT: E 303 PHE cc_start: 0.9409 (m-80) cc_final: 0.8798 (t80) REVERT: E 318 TYR cc_start: 0.8974 (t80) cc_final: 0.8453 (t80) REVERT: E 442 MET cc_start: 0.9624 (ttp) cc_final: 0.9359 (mtm) REVERT: E 513 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7569 (ttp) REVERT: E 597 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8677 (m-80) REVERT: E 799 MET cc_start: 0.9557 (tpp) cc_final: 0.9331 (tpp) REVERT: F 273 PHE cc_start: 0.9137 (m-80) cc_final: 0.8447 (m-80) REVERT: G 153 ASP cc_start: 0.9456 (t0) cc_final: 0.8988 (t0) REVERT: G 281 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9451 (tp) REVERT: G 285 MET cc_start: 0.9330 (mmt) cc_final: 0.8825 (mmm) REVERT: G 318 TYR cc_start: 0.9055 (t80) cc_final: 0.8558 (t80) REVERT: G 442 MET cc_start: 0.9598 (ttp) cc_final: 0.9184 (mtm) REVERT: G 460 MET cc_start: 0.9100 (mtp) cc_final: 0.8852 (tpp) REVERT: G 885 ASP cc_start: 0.9150 (p0) cc_final: 0.8843 (p0) REVERT: G 1009 MET cc_start: 0.8122 (mmm) cc_final: 0.7501 (mmm) REVERT: G 1049 ILE cc_start: 0.9721 (mt) cc_final: 0.9408 (tp) outliers start: 62 outliers final: 38 residues processed: 345 average time/residue: 0.1820 time to fit residues: 109.9734 Evaluate side-chains 340 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 194 PHE Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 555 GLU Chi-restraints excluded: chain E residue 597 PHE Chi-restraints excluded: chain E residue 946 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 1012 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 210 optimal weight: 30.0000 chunk 213 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 389 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 270 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 448 optimal weight: 0.4980 chunk 425 optimal weight: 20.0000 chunk 377 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 816 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN ** E 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 ASN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 816 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.050998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.034799 restraints weight = 234870.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.035827 restraints weight = 140578.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.036537 restraints weight = 98367.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.037040 restraints weight = 75962.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.037374 restraints weight = 62831.565| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 36376 Z= 0.103 Angle : 0.641 13.645 49436 Z= 0.297 Chirality : 0.041 0.357 5704 Planarity : 0.004 0.065 6264 Dihedral : 3.950 24.256 4872 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.32 % Allowed : 18.27 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.13), residues: 4504 helix: 1.14 (0.12), residues: 1904 sheet: -0.20 (0.24), residues: 504 loop : -0.23 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 113 TYR 0.016 0.001 TYR G 318 PHE 0.048 0.001 PHE G 223 TRP 0.018 0.001 TRP A 178 HIS 0.005 0.000 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00230 (36368) covalent geometry : angle 0.64073 (49420) SS BOND : bond 0.00174 ( 8) SS BOND : angle 1.01935 ( 16) hydrogen bonds : bond 0.03176 ( 1469) hydrogen bonds : angle 4.70781 ( 4113) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASP cc_start: 0.9473 (m-30) cc_final: 0.8980 (m-30) REVERT: A 303 PHE cc_start: 0.9481 (m-80) cc_final: 0.8979 (t80) REVERT: A 352 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9259 (p) REVERT: A 442 MET cc_start: 0.9586 (ttp) cc_final: 0.9254 (mtm) REVERT: A 460 MET cc_start: 0.8981 (tpp) cc_final: 0.8721 (tpp) REVERT: A 691 MET cc_start: 0.9602 (tpp) cc_final: 0.8696 (mmm) REVERT: A 794 ILE cc_start: 0.9595 (OUTLIER) cc_final: 0.9372 (mm) REVERT: A 830 MET cc_start: 0.9175 (mmt) cc_final: 0.8638 (mmm) REVERT: A 881 GLU cc_start: 0.9056 (tt0) cc_final: 0.8839 (tt0) REVERT: A 1009 MET cc_start: 0.8844 (mmm) cc_final: 0.8268 (mmm) REVERT: B 203 TRP cc_start: 0.8233 (t60) cc_final: 0.7695 (t-100) REVERT: C 104 MET cc_start: 0.8918 (mmm) cc_final: 0.8575 (mmm) REVERT: C 442 MET cc_start: 0.9598 (OUTLIER) cc_final: 0.9378 (mmm) REVERT: C 506 MET cc_start: 0.9298 (mmt) cc_final: 0.8854 (mmt) REVERT: C 510 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9302 (mm) REVERT: C 565 MET cc_start: 0.9348 (tpt) cc_final: 0.8984 (tpt) REVERT: C 691 MET cc_start: 0.9447 (mmm) cc_final: 0.9216 (tpp) REVERT: C 739 MET cc_start: 0.9617 (mtp) cc_final: 0.9296 (mtm) REVERT: C 830 MET cc_start: 0.9047 (mmm) cc_final: 0.8706 (mmt) REVERT: C 891 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9287 (mm) REVERT: C 1053 MET cc_start: 0.9108 (mtp) cc_final: 0.8872 (mmm) REVERT: D 273 PHE cc_start: 0.9352 (m-80) cc_final: 0.8976 (m-80) REVERT: D 277 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8802 (tt) REVERT: E 213 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8176 (mmm160) REVERT: E 223 PHE cc_start: 0.8973 (m-80) cc_final: 0.8561 (m-80) REVERT: E 252 PHE cc_start: 0.9450 (t80) cc_final: 0.9062 (t80) REVERT: E 303 PHE cc_start: 0.9397 (m-80) cc_final: 0.8782 (t80) REVERT: E 314 MET cc_start: 0.8593 (tmm) cc_final: 0.8379 (ppp) REVERT: E 318 TYR cc_start: 0.8969 (t80) cc_final: 0.8453 (t80) REVERT: E 388 GLU cc_start: 0.9350 (mt-10) cc_final: 0.9019 (mp0) REVERT: E 442 MET cc_start: 0.9605 (ttp) cc_final: 0.9363 (mtm) REVERT: E 513 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7672 (ttp) REVERT: E 597 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: F 172 LEU cc_start: 0.9528 (tp) cc_final: 0.9108 (mm) REVERT: F 273 PHE cc_start: 0.9101 (m-80) cc_final: 0.8415 (m-80) REVERT: G 153 ASP cc_start: 0.9463 (t0) cc_final: 0.9003 (t0) REVERT: G 281 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9418 (tp) REVERT: G 285 MET cc_start: 0.9324 (mmt) cc_final: 0.8850 (mmp) REVERT: G 318 TYR cc_start: 0.9019 (t80) cc_final: 0.8555 (t80) REVERT: G 442 MET cc_start: 0.9584 (ttp) cc_final: 0.9168 (mtm) REVERT: G 460 MET cc_start: 0.9129 (mtp) cc_final: 0.8901 (tpp) REVERT: G 499 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9348 (mm) REVERT: G 885 ASP cc_start: 0.9149 (p0) cc_final: 0.8853 (p0) REVERT: G 1009 MET cc_start: 0.8036 (mmm) cc_final: 0.7336 (mmm) REVERT: G 1049 ILE cc_start: 0.9713 (mt) cc_final: 0.9414 (tp) outliers start: 51 outliers final: 31 residues processed: 349 average time/residue: 0.1850 time to fit residues: 112.2257 Evaluate side-chains 335 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 555 GLU Chi-restraints excluded: chain E residue 597 PHE Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain E residue 946 THR Chi-restraints excluded: chain E residue 1012 PHE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 1012 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 445 optimal weight: 20.0000 chunk 393 optimal weight: 7.9990 chunk 241 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 364 optimal weight: 10.0000 chunk 390 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 233 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** 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 = 0.3289 r_free = 0.3289 target = 0.050070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.033879 restraints weight = 238764.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.034886 restraints weight = 143732.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.035598 restraints weight = 99830.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.036071 restraints weight = 77158.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.036419 restraints weight = 64034.360| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36376 Z= 0.130 Angle : 0.650 13.760 49436 Z= 0.305 Chirality : 0.041 0.367 5704 Planarity : 0.004 0.065 6264 Dihedral : 3.944 24.744 4872 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.11 % Allowed : 18.76 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4504 helix: 1.12 (0.12), residues: 1920 sheet: -0.38 (0.24), residues: 524 loop : -0.22 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 143 TYR 0.047 0.001 TYR A 163 PHE 0.051 0.001 PHE G 223 TRP 0.018 0.001 TRP A 178 HIS 0.005 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00292 (36368) covalent geometry : angle 0.64965 (49420) SS BOND : bond 0.00251 ( 8) SS BOND : angle 1.32618 ( 16) hydrogen bonds : bond 0.03230 ( 1469) hydrogen bonds : angle 4.75811 ( 4113) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9008 Ramachandran restraints generated. 4504 Oldfield, 0 Emsley, 4504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASP cc_start: 0.9505 (m-30) cc_final: 0.9019 (m-30) REVERT: A 257 GLU cc_start: 0.9615 (mm-30) cc_final: 0.8225 (pp20) REVERT: A 303 PHE cc_start: 0.9495 (m-80) cc_final: 0.9021 (t80) REVERT: A 352 THR cc_start: 0.9555 (OUTLIER) cc_final: 0.9222 (p) REVERT: A 442 MET cc_start: 0.9626 (ttp) cc_final: 0.9206 (mtm) REVERT: A 460 MET cc_start: 0.9007 (tpp) cc_final: 0.8597 (tpp) REVERT: A 691 MET cc_start: 0.9631 (tpp) cc_final: 0.8759 (mmm) REVERT: A 794 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9380 (mm) REVERT: A 830 MET cc_start: 0.9175 (mmt) cc_final: 0.8654 (mmm) REVERT: A 881 GLU cc_start: 0.9118 (tt0) cc_final: 0.8857 (tt0) REVERT: B 203 TRP cc_start: 0.8269 (t60) cc_final: 0.7702 (t-100) REVERT: C 104 MET cc_start: 0.8914 (mmm) cc_final: 0.8698 (mmm) REVERT: C 506 MET cc_start: 0.9278 (mmt) cc_final: 0.8875 (mmt) REVERT: C 510 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9335 (mm) REVERT: C 565 MET cc_start: 0.9371 (tpt) cc_final: 0.8882 (tpt) REVERT: C 691 MET cc_start: 0.9451 (mmm) cc_final: 0.8589 (mmm) REVERT: C 739 MET cc_start: 0.9623 (mtp) cc_final: 0.9325 (mtm) REVERT: C 830 MET cc_start: 0.9020 (mmm) cc_final: 0.8515 (mmt) REVERT: C 891 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9299 (mm) REVERT: C 1053 MET cc_start: 0.9099 (mtp) cc_final: 0.8847 (mmm) REVERT: D 273 PHE cc_start: 0.9366 (m-80) cc_final: 0.9019 (m-80) REVERT: D 277 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8807 (tt) REVERT: E 153 ASP cc_start: 0.9704 (t0) cc_final: 0.9493 (t0) REVERT: E 154 MET cc_start: 0.9577 (tpt) cc_final: 0.8958 (mmm) REVERT: E 213 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8167 (mmm160) REVERT: E 223 PHE cc_start: 0.8957 (m-80) cc_final: 0.8527 (m-80) REVERT: E 252 PHE cc_start: 0.9433 (t80) cc_final: 0.9049 (t80) REVERT: E 303 PHE cc_start: 0.9422 (m-80) cc_final: 0.8843 (t80) REVERT: E 314 MET cc_start: 0.8566 (tmm) cc_final: 0.8306 (tmm) REVERT: E 318 TYR cc_start: 0.9028 (t80) cc_final: 0.8487 (t80) REVERT: E 442 MET cc_start: 0.9639 (ttp) cc_final: 0.9377 (mtm) REVERT: E 513 MET cc_start: 0.8106 (ttp) cc_final: 0.7677 (ttp) REVERT: E 597 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8694 (m-80) REVERT: E 885 ASP cc_start: 0.9100 (p0) cc_final: 0.8888 (p0) REVERT: F 172 LEU cc_start: 0.9552 (tp) cc_final: 0.9132 (mm) REVERT: F 273 PHE cc_start: 0.9122 (m-80) cc_final: 0.8451 (m-80) REVERT: G 153 ASP cc_start: 0.9482 (t0) cc_final: 0.9029 (t0) REVERT: G 281 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9432 (tp) REVERT: G 285 MET cc_start: 0.9319 (mmt) cc_final: 0.8836 (mmp) REVERT: G 318 TYR cc_start: 0.9016 (t80) cc_final: 0.8562 (t80) REVERT: G 442 MET cc_start: 0.9603 (ttp) cc_final: 0.9185 (mtm) REVERT: G 460 MET cc_start: 0.9128 (mtp) cc_final: 0.8822 (tpp) REVERT: G 499 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9361 (mm) REVERT: G 885 ASP cc_start: 0.9143 (p0) cc_final: 0.8840 (p0) REVERT: G 1009 MET cc_start: 0.8110 (mmm) cc_final: 0.7447 (mmm) REVERT: G 1049 ILE cc_start: 0.9718 (mt) cc_final: 0.9415 (tp) REVERT: G 1053 MET cc_start: 0.8986 (mmm) cc_final: 0.8707 (mmm) outliers start: 43 outliers final: 31 residues processed: 324 average time/residue: 0.1873 time to fit residues: 105.6163 Evaluate side-chains 328 residues out of total 3876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 555 GLU Chi-restraints excluded: chain E residue 597 PHE Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain E residue 1012 PHE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 598 ILE Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 1012 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 155 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 194 optimal weight: 30.0000 chunk 98 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 382 optimal weight: 9.9990 chunk 415 optimal weight: 6.9990 chunk 433 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN ** E 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.049238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032954 restraints weight = 241383.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.033957 restraints weight = 147301.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.034582 restraints weight = 102813.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.035093 restraints weight = 80503.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.035455 restraints weight = 66470.932| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36376 Z= 0.157 Angle : 0.660 13.538 49436 Z= 0.312 Chirality : 0.041 0.346 5704 Planarity : 0.004 0.066 6264 Dihedral : 3.998 24.719 4872 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.14 % Allowed : 18.81 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4504 helix: 1.11 (0.12), residues: 1920 sheet: -0.38 (0.24), residues: 524 loop : -0.20 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 960 TYR 0.026 0.001 TYR G 274 PHE 0.048 0.001 PHE G 223 TRP 0.020 0.001 TRP A 178 HIS 0.005 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00341 (36368) covalent geometry : angle 0.66003 (49420) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.29392 ( 16) hydrogen bonds : bond 0.03285 ( 1469) hydrogen bonds : angle 4.82611 ( 4113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5398.74 seconds wall clock time: 94 minutes 30.35 seconds (5670.35 seconds total)