Starting phenix.real_space_refine on Sat Mar 7 03:01:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dd9_30650/03_2026/7dd9_30650.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dd9_30650/03_2026/7dd9_30650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dd9_30650/03_2026/7dd9_30650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dd9_30650/03_2026/7dd9_30650.map" model { file = "/net/cci-nas-00/data/ceres_data/7dd9_30650/03_2026/7dd9_30650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dd9_30650/03_2026/7dd9_30650.cif" } resolution = 2.4 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 12 6.06 5 S 192 5.16 5 C 23108 2.51 5 N 6112 2.21 5 O 7725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 220 residue(s): 0.04s 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: 37149 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 238 Classifications: {'water': 238} Link IDs: {None: 237} Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 238 Classifications: {'water': 238} Link IDs: {None: 237} Chain: "E" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 236 Classifications: {'water': 236} Link IDs: {None: 235} Chain: "G" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 237 Classifications: {'water': 237} Link IDs: {None: 236} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8784 SG CYS A2076 57.136 17.348 112.716 1.00 67.55 S ATOM 8806 SG CYS A2079 58.571 20.770 111.901 1.00 61.12 S ATOM 8964 SG CYS A2098 54.943 19.942 110.708 1.00 57.85 S ATOM 8670 SG CYS A2062 60.164 21.026 124.647 1.00 67.75 S ATOM 8691 SG CYS A2065 60.430 22.029 128.294 1.00 67.69 S ATOM 8857 SG CYS A2085 60.746 18.329 127.295 1.00 76.17 S ATOM 8882 SG CYS A2088 57.427 20.165 127.193 1.00 76.07 S ATOM 17831 SG CYS C2076 80.151 97.083 112.724 1.00 67.74 S ATOM 17853 SG CYS C2079 78.696 93.674 111.891 1.00 61.44 S ATOM 18011 SG CYS C2098 82.328 94.489 110.699 1.00 58.32 S ATOM 17717 SG CYS C2062 77.118 93.351 124.637 1.00 67.91 S ATOM 17738 SG CYS C2065 76.851 92.328 128.279 1.00 67.52 S ATOM 17904 SG CYS C2085 76.553 96.035 127.301 1.00 76.38 S ATOM 17929 SG CYS C2088 79.863 94.182 127.184 1.00 76.34 S ATOM 26878 SG CYS E2076 80.147 17.333 55.758 1.00 67.63 S ATOM 26900 SG CYS E2079 78.704 20.750 56.580 1.00 61.32 S ATOM 27058 SG CYS E2098 82.334 19.927 57.774 1.00 58.11 S ATOM 26764 SG CYS E2062 77.121 21.033 43.834 1.00 68.10 S ATOM 26785 SG CYS E2065 76.856 22.044 40.189 1.00 67.91 S ATOM 26951 SG CYS E2085 76.546 18.341 41.179 1.00 76.34 S ATOM 26976 SG CYS E2088 79.862 20.183 41.288 1.00 76.30 S ATOM 35925 SG CYS G2076 57.107 97.066 55.731 1.00 67.77 S ATOM 35947 SG CYS G2079 58.554 93.653 56.560 1.00 61.52 S ATOM 36105 SG CYS G2098 54.920 94.470 57.742 1.00 57.91 S ATOM 35811 SG CYS G2062 60.177 93.362 43.819 1.00 68.08 S ATOM 35832 SG CYS G2065 60.455 92.349 40.175 1.00 67.95 S ATOM 35998 SG CYS G2085 60.755 96.052 41.163 1.00 76.40 S ATOM 36023 SG CYS G2088 57.442 94.204 41.264 1.00 76.26 S Time building chain proxies: 8.17, per 1000 atoms: 0.22 Number of scatterers: 37149 At special positions: 0 Unit cell: (138.32, 115.44, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 12 29.99 S 192 16.00 O 7725 8.00 N 6112 7.00 C 23108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 615 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 290 " pdb=" ZN A1602 " pdb="ZN ZN A1602 " - pdb=" NE2 HIS A2096 " pdb="ZN ZN A1602 " - pdb=" SG CYS A2076 " pdb="ZN ZN A1602 " - pdb=" SG CYS A2079 " pdb="ZN ZN A1602 " - pdb=" SG CYS A2098 " pdb=" ZN A1603 " pdb="ZN ZN A1603 " - pdb=" SG CYS A2065 " pdb="ZN ZN A1603 " - pdb=" SG CYS A2088 " pdb="ZN ZN A1603 " - pdb=" SG CYS A2062 " pdb="ZN ZN A1603 " - pdb=" SG CYS A2085 " pdb=" ZN C1601 " pdb="ZN ZN C1601 " - pdb=" NE2 HIS C 615 " pdb="ZN ZN C1601 " - pdb=" NE2 HIS C 290 " pdb=" ZN C1602 " pdb="ZN ZN C1602 " - pdb=" NE2 HIS C2096 " pdb="ZN ZN C1602 " - pdb=" SG CYS C2076 " pdb="ZN ZN C1602 " - pdb=" SG CYS C2079 " pdb="ZN ZN C1602 " - pdb=" SG CYS C2098 " pdb=" ZN C1603 " pdb="ZN ZN C1603 " - pdb=" SG CYS C2065 " pdb="ZN ZN C1603 " - pdb=" SG CYS C2088 " pdb="ZN ZN C1603 " - pdb=" SG CYS C2062 " pdb="ZN ZN C1603 " - pdb=" SG CYS C2085 " pdb=" ZN E1601 " pdb="ZN ZN E1601 " - pdb=" NE2 HIS E 615 " pdb="ZN ZN E1601 " - pdb=" NE2 HIS E 290 " pdb=" ZN E1602 " pdb="ZN ZN E1602 " - pdb=" NE2 HIS E2096 " pdb="ZN ZN E1602 " - pdb=" SG CYS E2076 " pdb="ZN ZN E1602 " - pdb=" SG CYS E2079 " pdb="ZN ZN E1602 " - pdb=" SG CYS E2098 " pdb=" ZN E1603 " pdb="ZN ZN E1603 " - pdb=" SG CYS E2065 " pdb="ZN ZN E1603 " - pdb=" SG CYS E2088 " pdb="ZN ZN E1603 " - pdb=" SG CYS E2062 " pdb="ZN ZN E1603 " - pdb=" SG CYS E2085 " pdb=" ZN G1601 " pdb="ZN ZN G1601 " - pdb=" NE2 HIS G 615 " pdb="ZN ZN G1601 " - pdb=" NE2 HIS G 290 " pdb=" ZN G1602 " pdb="ZN ZN G1602 " - pdb=" NE2 HIS G2096 " pdb="ZN ZN G1602 " - pdb=" SG CYS G2076 " pdb="ZN ZN G1602 " - pdb=" SG CYS G2079 " pdb="ZN ZN G1602 " - pdb=" SG CYS G2098 " pdb=" ZN G1603 " pdb="ZN ZN G1603 " - pdb=" SG CYS G2065 " pdb="ZN ZN G1603 " - pdb=" SG CYS G2088 " pdb="ZN ZN G1603 " - pdb=" SG CYS G2062 " pdb="ZN ZN G1603 " - pdb=" SG CYS G2085 " Number of angles added : 36 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8544 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 48 sheets defined 30.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 33 through 42 removed outlier: 6.836A pdb=" N LEU A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Proline residue: A 39 - end of helix removed outlier: 3.526A pdb=" N TYR A 42 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 113 through 118 removed outlier: 4.113A pdb=" N LYS A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.805A pdb=" N TYR A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.033A pdb=" N ASN A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 4.011A pdb=" N VAL A 273 " --> pdb=" O SER A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.716A pdb=" N ARG A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 465 through 475 removed outlier: 3.931A pdb=" N ILE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.501A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 539 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 564 through 592 Processing helix chain 'A' and resid 598 through 612 Processing helix chain 'A' and resid 623 through 653 removed outlier: 3.638A pdb=" N TYR A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) Proline residue: A 632 - end of helix Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 780 through 785 removed outlier: 3.672A pdb=" N LEU A 784 " --> pdb=" O VAL A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 882 through 888 removed outlier: 3.667A pdb=" N LYS A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 968 removed outlier: 3.685A pdb=" N VAL A 961 " --> pdb=" O ASP A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 2086 through 2091 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 24 through 27 Processing helix chain 'C' and resid 33 through 42 removed outlier: 6.836A pdb=" N LEU C 38 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Proline residue: C 39 - end of helix removed outlier: 3.526A pdb=" N TYR C 42 " --> pdb=" O PRO C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 Processing helix chain 'C' and resid 113 through 118 removed outlier: 4.113A pdb=" N LYS C 118 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 224 Processing helix chain 'C' and resid 228 through 245 removed outlier: 3.806A pdb=" N TYR C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 265 removed outlier: 4.032A pdb=" N ASN C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 removed outlier: 4.012A pdb=" N VAL C 273 " --> pdb=" O SER C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.717A pdb=" N ARG C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'C' and resid 340 through 353 Processing helix chain 'C' and resid 372 through 391 Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 465 through 475 removed outlier: 3.932A pdb=" N ILE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 516 removed outlier: 3.501A pdb=" N LEU C 503 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 539 Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 564 through 592 Processing helix chain 'C' and resid 598 through 612 Processing helix chain 'C' and resid 623 through 653 removed outlier: 3.638A pdb=" N TYR C 627 " --> pdb=" O ILE C 623 " (cutoff:3.500A) Proline residue: C 632 - end of helix Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 780 through 785 removed outlier: 3.672A pdb=" N LEU C 784 " --> pdb=" O VAL C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 834 Processing helix chain 'C' and resid 882 through 888 removed outlier: 3.667A pdb=" N LYS C 888 " --> pdb=" O TRP C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 968 removed outlier: 3.685A pdb=" N VAL C 961 " --> pdb=" O ASP C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 2086 through 2091 Processing helix chain 'E' and resid 16 through 23 Processing helix chain 'E' and resid 24 through 27 Processing helix chain 'E' and resid 33 through 42 removed outlier: 6.836A pdb=" N LEU E 38 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Proline residue: E 39 - end of helix removed outlier: 3.526A pdb=" N TYR E 42 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 Processing helix chain 'E' and resid 113 through 118 removed outlier: 4.113A pdb=" N LYS E 118 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 224 Processing helix chain 'E' and resid 228 through 245 removed outlier: 3.806A pdb=" N TYR E 232 " --> pdb=" O CYS E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.032A pdb=" N ASN E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 276 removed outlier: 4.011A pdb=" N VAL E 273 " --> pdb=" O SER E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 320 removed outlier: 3.717A pdb=" N ARG E 304 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL E 307 " --> pdb=" O ARG E 303 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR E 312 " --> pdb=" O ARG E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 340 Processing helix chain 'E' and resid 340 through 353 Processing helix chain 'E' and resid 372 through 391 Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'E' and resid 425 through 430 Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.931A pdb=" N ILE E 473 " --> pdb=" O VAL E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 516 removed outlier: 3.501A pdb=" N LEU E 503 " --> pdb=" O THR E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 539 Processing helix chain 'E' and resid 557 through 562 Processing helix chain 'E' and resid 564 through 592 Processing helix chain 'E' and resid 598 through 612 Processing helix chain 'E' and resid 623 through 653 removed outlier: 3.638A pdb=" N TYR E 627 " --> pdb=" O ILE E 623 " (cutoff:3.500A) Proline residue: E 632 - end of helix Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 780 through 785 removed outlier: 3.672A pdb=" N LEU E 784 " --> pdb=" O VAL E 781 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 834 Processing helix chain 'E' and resid 882 through 888 removed outlier: 3.669A pdb=" N LYS E 888 " --> pdb=" O TRP E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 957 through 968 removed outlier: 3.685A pdb=" N VAL E 961 " --> pdb=" O ASP E 957 " (cutoff:3.500A) Processing helix chain 'E' and resid 2086 through 2091 Processing helix chain 'G' and resid 16 through 23 Processing helix chain 'G' and resid 24 through 27 Processing helix chain 'G' and resid 33 through 42 removed outlier: 6.835A pdb=" N LEU G 38 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Proline residue: G 39 - end of helix removed outlier: 3.526A pdb=" N TYR G 42 " --> pdb=" O PRO G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 113 through 118 removed outlier: 4.114A pdb=" N LYS G 118 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 224 Processing helix chain 'G' and resid 228 through 245 removed outlier: 3.804A pdb=" N TYR G 232 " --> pdb=" O CYS G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 265 removed outlier: 4.032A pdb=" N ASN G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA G 262 " --> pdb=" O ASN G 258 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE G 263 " --> pdb=" O LEU G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 276 removed outlier: 4.011A pdb=" N VAL G 273 " --> pdb=" O SER G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 320 removed outlier: 3.717A pdb=" N ARG G 304 " --> pdb=" O ALA G 300 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 307 " --> pdb=" O ARG G 303 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR G 312 " --> pdb=" O ARG G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 340 Processing helix chain 'G' and resid 340 through 353 Processing helix chain 'G' and resid 372 through 391 Processing helix chain 'G' and resid 409 through 417 Processing helix chain 'G' and resid 425 through 430 Processing helix chain 'G' and resid 465 through 475 removed outlier: 3.931A pdb=" N ILE G 473 " --> pdb=" O VAL G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 516 Processing helix chain 'G' and resid 527 through 539 Processing helix chain 'G' and resid 557 through 562 Processing helix chain 'G' and resid 564 through 592 Processing helix chain 'G' and resid 598 through 612 Processing helix chain 'G' and resid 623 through 653 removed outlier: 3.638A pdb=" N TYR G 627 " --> pdb=" O ILE G 623 " (cutoff:3.500A) Proline residue: G 632 - end of helix Processing helix chain 'G' and resid 662 through 664 No H-bonds generated for 'chain 'G' and resid 662 through 664' Processing helix chain 'G' and resid 780 through 785 removed outlier: 3.671A pdb=" N LEU G 784 " --> pdb=" O VAL G 781 " (cutoff:3.500A) Processing helix chain 'G' and resid 830 through 834 Processing helix chain 'G' and resid 882 through 888 removed outlier: 3.668A pdb=" N LYS G 888 " --> pdb=" O TRP G 884 " (cutoff:3.500A) Processing helix chain 'G' and resid 957 through 968 removed outlier: 3.685A pdb=" N VAL G 961 " --> pdb=" O ASP G 957 " (cutoff:3.500A) Processing helix chain 'G' and resid 2086 through 2091 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.991A pdb=" N GLU A 89 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 65 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN A 143 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.622A pdb=" N PHE A 193 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.264A pdb=" N PHE A 325 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL A 326 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY A 287 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 284 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE A 489 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A 286 " --> pdb=" O PHE A 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.264A pdb=" N PHE A 325 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL A 326 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY A 287 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 399 Processing sheet with id=AA6, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.685A pdb=" N ARG A 972 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU A 666 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AA8, first strand: chain 'A' and resid 787 through 790 removed outlier: 4.680A pdb=" N TYR A 764 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS A 850 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG A 929 " --> pdb=" O LYS A 850 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 852 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 922 " --> pdb=" O HIS A 919 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY A 915 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 794 through 800 removed outlier: 6.505A pdb=" N SER A 806 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER A 800 " --> pdb=" O ARG A 804 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE A 896 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER A 900 " --> pdb=" O PHE A 864 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE A 864 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 989 through 993 Processing sheet with id=AB2, first strand: chain 'A' and resid 997 through 1004 removed outlier: 5.521A pdb=" N LEU A 999 " --> pdb=" O TYR A1016 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A1016 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A1072 " --> pdb=" O CYS A1040 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A1037 " --> pdb=" O GLU A1049 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU A1049 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS A1039 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2083 through 2085 Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.991A pdb=" N GLU C 89 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU C 65 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 143 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.621A pdb=" N PHE C 193 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE C 325 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL C 326 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY C 287 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE C 284 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE C 489 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE C 286 " --> pdb=" O PHE C 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE C 325 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL C 326 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY C 287 " --> pdb=" O VAL C 326 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 397 through 399 Processing sheet with id=AB9, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.685A pdb=" N ARG C 972 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU C 666 " --> pdb=" O ALA C 702 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AC2, first strand: chain 'C' and resid 787 through 790 removed outlier: 4.680A pdb=" N TYR C 764 " --> pdb=" O LEU C 790 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS C 850 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG C 929 " --> pdb=" O LYS C 850 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 852 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 922 " --> pdb=" O HIS C 919 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY C 915 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 794 through 800 removed outlier: 6.505A pdb=" N SER C 806 " --> pdb=" O LYS C 798 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C 800 " --> pdb=" O ARG C 804 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG C 804 " --> pdb=" O SER C 800 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER C 817 " --> pdb=" O ILE C 813 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE C 896 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER C 900 " --> pdb=" O PHE C 864 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE C 864 " --> pdb=" O SER C 900 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 989 through 993 Processing sheet with id=AC5, first strand: chain 'C' and resid 997 through 1004 removed outlier: 5.465A pdb=" N LEU C 999 " --> pdb=" O TYR C1016 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR C1016 " --> pdb=" O LEU C 999 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR C1072 " --> pdb=" O CYS C1040 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL C1037 " --> pdb=" O GLU C1049 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU C1049 " --> pdb=" O VAL C1037 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS C1039 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 2083 through 2085 Processing sheet with id=AC7, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.992A pdb=" N GLU E 89 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU E 65 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN E 143 " --> pdb=" O VAL E 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.621A pdb=" N PHE E 193 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE E 325 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL E 326 " --> pdb=" O ALA E 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY E 287 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE E 284 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE E 489 " --> pdb=" O PHE E 284 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE E 286 " --> pdb=" O PHE E 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE E 325 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL E 326 " --> pdb=" O ALA E 285 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY E 287 " --> pdb=" O VAL E 326 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 397 through 399 Processing sheet with id=AD3, first strand: chain 'E' and resid 654 through 656 removed outlier: 3.685A pdb=" N ARG E 972 " --> pdb=" O LEU E 669 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU E 666 " --> pdb=" O ALA E 702 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 712 through 715 Processing sheet with id=AD5, first strand: chain 'E' and resid 787 through 790 removed outlier: 4.679A pdb=" N TYR E 764 " --> pdb=" O LEU E 790 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS E 850 " --> pdb=" O ARG E 929 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG E 929 " --> pdb=" O LYS E 850 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU E 852 " --> pdb=" O LEU E 927 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 922 " --> pdb=" O HIS E 919 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY E 915 " --> pdb=" O SER E 926 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 794 through 800 removed outlier: 6.505A pdb=" N SER E 806 " --> pdb=" O LYS E 798 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER E 800 " --> pdb=" O ARG E 804 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG E 804 " --> pdb=" O SER E 800 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER E 817 " --> pdb=" O ILE E 813 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE E 896 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER E 900 " --> pdb=" O PHE E 864 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE E 864 " --> pdb=" O SER E 900 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 989 through 993 Processing sheet with id=AD8, first strand: chain 'E' and resid 997 through 1004 removed outlier: 5.465A pdb=" N LEU E 999 " --> pdb=" O TYR E1016 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR E1016 " --> pdb=" O LEU E 999 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR E1072 " --> pdb=" O CYS E1040 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL E1037 " --> pdb=" O GLU E1049 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU E1049 " --> pdb=" O VAL E1037 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS E1039 " --> pdb=" O LEU E1047 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 2083 through 2085 Processing sheet with id=AE1, first strand: chain 'G' and resid 89 through 91 removed outlier: 3.991A pdb=" N GLU G 89 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU G 65 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN G 143 " --> pdb=" O VAL G 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 96 through 97 removed outlier: 3.621A pdb=" N PHE G 193 " --> pdb=" O PHE G 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE G 325 " --> pdb=" O ILE G 357 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL G 326 " --> pdb=" O ALA G 285 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY G 287 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE G 284 " --> pdb=" O LEU G 487 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE G 489 " --> pdb=" O PHE G 284 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE G 286 " --> pdb=" O PHE G 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 357 through 358 removed outlier: 6.265A pdb=" N PHE G 325 " --> pdb=" O ILE G 357 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL G 326 " --> pdb=" O ALA G 285 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY G 287 " --> pdb=" O VAL G 326 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 397 through 399 Processing sheet with id=AE6, first strand: chain 'G' and resid 654 through 656 removed outlier: 3.685A pdb=" N ARG G 972 " --> pdb=" O LEU G 669 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU G 666 " --> pdb=" O ALA G 702 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 712 through 715 Processing sheet with id=AE8, first strand: chain 'G' and resid 787 through 790 removed outlier: 4.681A pdb=" N TYR G 764 " --> pdb=" O LEU G 790 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS G 850 " --> pdb=" O ARG G 929 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG G 929 " --> pdb=" O LYS G 850 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU G 852 " --> pdb=" O LEU G 927 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 922 " --> pdb=" O HIS G 919 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY G 915 " --> pdb=" O SER G 926 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 794 through 800 removed outlier: 6.504A pdb=" N SER G 806 " --> pdb=" O LYS G 798 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER G 800 " --> pdb=" O ARG G 804 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG G 804 " --> pdb=" O SER G 800 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER G 817 " --> pdb=" O ILE G 813 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE G 896 " --> pdb=" O GLU G 868 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER G 900 " --> pdb=" O PHE G 864 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE G 864 " --> pdb=" O SER G 900 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 989 through 993 Processing sheet with id=AF2, first strand: chain 'G' and resid 997 through 1004 removed outlier: 5.465A pdb=" N LEU G 999 " --> pdb=" O TYR G1016 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR G1016 " --> pdb=" O LEU G 999 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR G1072 " --> pdb=" O CYS G1040 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL G1037 " --> pdb=" O GLU G1049 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU G1049 " --> pdb=" O VAL G1037 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS G1039 " --> pdb=" O LEU G1047 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 2083 through 2085 1549 hydrogen bonds defined for protein. 4203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.56 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11737 1.34 - 1.46: 7677 1.46 - 1.58: 17450 1.58 - 1.70: 0 1.70 - 1.81: 260 Bond restraints: 37124 Sorted by residual: bond pdb=" CB MET A 242 " pdb=" CG MET A 242 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.58e+00 bond pdb=" CB MET E 242 " pdb=" CG MET E 242 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.58e+00 bond pdb=" CB MET G 242 " pdb=" CG MET G 242 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.46e+00 bond pdb=" CB MET C 242 " pdb=" CG MET C 242 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.46e+00 bond pdb=" SD MET G 242 " pdb=" CE MET G 242 " ideal model delta sigma weight residual 1.791 1.736 0.055 2.50e-02 1.60e+03 4.88e+00 ... (remaining 37119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 49271 2.02 - 4.04: 915 4.04 - 6.05: 151 6.05 - 8.07: 20 8.07 - 10.09: 15 Bond angle restraints: 50372 Sorted by residual: angle pdb=" N GLU E1017 " pdb=" CA GLU E1017 " pdb=" C GLU E1017 " ideal model delta sigma weight residual 109.76 101.24 8.52 1.59e+00 3.96e-01 2.87e+01 angle pdb=" N GLU C1017 " pdb=" CA GLU C1017 " pdb=" C GLU C1017 " ideal model delta sigma weight residual 109.76 101.27 8.49 1.59e+00 3.96e-01 2.85e+01 angle pdb=" N GLU G1017 " pdb=" CA GLU G1017 " pdb=" C GLU G1017 " ideal model delta sigma weight residual 109.76 101.29 8.47 1.59e+00 3.96e-01 2.84e+01 angle pdb=" N ASP A 742 " pdb=" CA ASP A 742 " pdb=" C ASP A 742 " ideal model delta sigma weight residual 109.76 102.73 7.03 1.59e+00 3.96e-01 1.95e+01 angle pdb=" N ASP E 742 " pdb=" CA ASP E 742 " pdb=" C ASP E 742 " ideal model delta sigma weight residual 109.76 102.74 7.02 1.59e+00 3.96e-01 1.95e+01 ... (remaining 50367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 19341 17.85 - 35.69: 2084 35.69 - 53.54: 483 53.54 - 71.38: 76 71.38 - 89.23: 44 Dihedral angle restraints: 22028 sinusoidal: 8820 harmonic: 13208 Sorted by residual: dihedral pdb=" CA TYR A 42 " pdb=" C TYR A 42 " pdb=" N ASP A 43 " pdb=" CA ASP A 43 " ideal model delta harmonic sigma weight residual -180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA TYR G 42 " pdb=" C TYR G 42 " pdb=" N ASP G 43 " pdb=" CA ASP G 43 " ideal model delta harmonic sigma weight residual 180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA TYR C 42 " pdb=" C TYR C 42 " pdb=" N ASP C 43 " pdb=" CA ASP C 43 " ideal model delta harmonic sigma weight residual -180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 22025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3624 0.047 - 0.094: 1407 0.094 - 0.141: 398 0.141 - 0.189: 27 0.189 - 0.236: 8 Chirality restraints: 5464 Sorted by residual: chirality pdb=" CA GLU E1017 " pdb=" N GLU E1017 " pdb=" C GLU E1017 " pdb=" CB GLU E1017 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA GLU G1017 " pdb=" N GLU G1017 " pdb=" C GLU G1017 " pdb=" CB GLU G1017 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA GLU C1017 " pdb=" N GLU C1017 " pdb=" C GLU C1017 " pdb=" CB GLU C1017 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 5461 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 159 " -0.022 2.00e-02 2.50e+03 1.14e-02 3.25e+00 pdb=" CG TRP A 159 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 159 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 159 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 159 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 159 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 159 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 159 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 159 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 159 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 159 " 0.022 2.00e-02 2.50e+03 1.14e-02 3.22e+00 pdb=" CG TRP E 159 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP E 159 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP E 159 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP E 159 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 159 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 159 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 159 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 159 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 159 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 159 " -0.022 2.00e-02 2.50e+03 1.12e-02 3.16e+00 pdb=" CG TRP G 159 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP G 159 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP G 159 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP G 159 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 159 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 159 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 159 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 159 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 159 " -0.003 2.00e-02 2.50e+03 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 417 2.53 - 3.12: 28351 3.12 - 3.71: 63155 3.71 - 4.31: 100637 4.31 - 4.90: 155639 Nonbonded interactions: 348199 Sorted by model distance: nonbonded pdb=" OD2 ASP C 402 " pdb="ZN ZN C1601 " model vdw 1.932 2.230 nonbonded pdb=" OD2 ASP G 402 " pdb="ZN ZN G1601 " model vdw 1.933 2.230 nonbonded pdb=" OD2 ASP A 402 " pdb="ZN ZN A1601 " model vdw 1.933 2.230 nonbonded pdb=" OD2 ASP E 402 " pdb="ZN ZN E1601 " model vdw 1.933 2.230 nonbonded pdb=" OD1 ASP E 292 " pdb="ZN ZN E1601 " model vdw 1.986 2.230 ... (remaining 348194 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 40.970 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.007 0.077 37164 Z= 0.318 Angle : 0.714 10.089 50408 Z= 0.391 Chirality : 0.052 0.236 5464 Planarity : 0.004 0.044 6516 Dihedral : 15.884 89.231 13484 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.93 % Allowed : 16.57 % Favored : 81.50 % 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: -1.19 (0.12), residues: 4500 helix: 0.77 (0.15), residues: 1156 sheet: -0.39 (0.14), residues: 1136 loop : -1.90 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1026 TYR 0.021 0.002 TYR G 627 PHE 0.019 0.002 PHE C 325 TRP 0.026 0.002 TRP A 159 HIS 0.005 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00737 (37124) covalent geometry : angle 0.71090 (50372) hydrogen bonds : bond 0.13428 ( 1549) hydrogen bonds : angle 6.38577 ( 4203) metal coordination : bond 0.00621 ( 40) metal coordination : angle 2.41905 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 322 time to evaluate : 1.539 Fit side-chains REVERT: A 48 ASP cc_start: 0.7674 (p0) cc_final: 0.7411 (p0) REVERT: C 48 ASP cc_start: 0.7685 (p0) cc_final: 0.7414 (p0) REVERT: E 48 ASP cc_start: 0.7684 (p0) cc_final: 0.7408 (p0) REVERT: G 48 ASP cc_start: 0.7683 (p0) cc_final: 0.7408 (p0) outliers start: 77 outliers final: 51 residues processed: 396 average time/residue: 0.7910 time to fit residues: 372.9074 Evaluate side-chains 337 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 2084 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 543 GLN Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain C residue 1057 ASP Chi-restraints excluded: chain C residue 2084 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 824 SER Chi-restraints excluded: chain E residue 953 SER Chi-restraints excluded: chain E residue 987 ASP Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1057 ASP Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 466 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 596 SER Chi-restraints excluded: chain G residue 824 SER Chi-restraints excluded: chain G residue 953 SER Chi-restraints excluded: chain G residue 987 ASP Chi-restraints excluded: chain G residue 1056 ASN Chi-restraints excluded: chain G residue 1057 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 0.0670 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0020 chunk 132 optimal weight: 0.0050 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 0.8980 overall best weight: 0.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 248 ASN A 665 GLN A 744 HIS A 775 GLN A 894 GLN A 921 ASN A1076 ASN C 236 GLN C 248 ASN C 665 GLN C 744 HIS C 775 GLN C 894 GLN C 921 ASN C1076 ASN E 236 GLN E 248 ASN E 665 GLN E 744 HIS E 775 GLN E 894 GLN E 921 ASN E1076 ASN G 236 GLN G 248 ASN G 665 GLN G 744 HIS G 775 GLN G 894 GLN G 921 ASN G1076 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105616 restraints weight = 37163.524| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.42 r_work: 0.2992 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 37164 Z= 0.120 Angle : 0.573 6.922 50408 Z= 0.310 Chirality : 0.045 0.171 5464 Planarity : 0.004 0.034 6516 Dihedral : 6.833 58.047 4923 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.05 % Allowed : 15.82 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4500 helix: 1.04 (0.15), residues: 1168 sheet: -0.51 (0.15), residues: 1104 loop : -1.71 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.015 0.001 TYR E 627 PHE 0.017 0.001 PHE E 896 TRP 0.013 0.001 TRP C 777 HIS 0.003 0.001 HIS E 615 Details of bonding type rmsd covalent geometry : bond 0.00249 (37124) covalent geometry : angle 0.57105 (50372) hydrogen bonds : bond 0.04234 ( 1549) hydrogen bonds : angle 5.39627 ( 4203) metal coordination : bond 0.00516 ( 40) metal coordination : angle 2.05149 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 360 time to evaluate : 1.447 Fit side-chains REVERT: A 46 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7399 (ttm-80) REVERT: A 236 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8469 (tm130) REVERT: A 278 ASN cc_start: 0.8259 (p0) cc_final: 0.7988 (p0) REVERT: A 423 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8977 (tm) REVERT: C 46 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7414 (ttm-80) REVERT: C 236 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8459 (tm130) REVERT: C 278 ASN cc_start: 0.8270 (p0) cc_final: 0.8005 (p0) REVERT: C 423 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8968 (tm) REVERT: E 46 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7407 (ttm-80) REVERT: E 236 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8456 (tm130) REVERT: E 278 ASN cc_start: 0.8268 (p0) cc_final: 0.7997 (p0) REVERT: E 423 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8982 (tm) REVERT: E 677 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7677 (mtt-85) REVERT: G 46 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7403 (ttm-80) REVERT: G 236 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8457 (tm130) REVERT: G 278 ASN cc_start: 0.8261 (p0) cc_final: 0.7989 (p0) REVERT: G 423 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8982 (tm) outliers start: 122 outliers final: 20 residues processed: 447 average time/residue: 0.8016 time to fit residues: 427.9226 Evaluate side-chains 337 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 309 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 831 CYS Chi-restraints excluded: chain G residue 1056 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 111 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 402 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 397 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 329 GLN A 775 GLN A 921 ASN C 248 ASN C 329 GLN C 775 GLN C 921 ASN C 996 ASN E 248 ASN E 329 GLN E 775 GLN E 921 ASN E 996 ASN G 248 ASN G 329 GLN G 775 GLN G 921 ASN G 996 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.098327 restraints weight = 36345.180| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.48 r_work: 0.2871 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 37164 Z= 0.343 Angle : 0.741 14.183 50408 Z= 0.396 Chirality : 0.054 0.198 5464 Planarity : 0.006 0.072 6516 Dihedral : 6.706 40.794 4864 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.23 % Allowed : 15.03 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.12), residues: 4500 helix: 0.88 (0.15), residues: 1160 sheet: -0.62 (0.14), residues: 1116 loop : -1.80 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 572 TYR 0.027 0.003 TYR A 406 PHE 0.019 0.003 PHE A1073 TRP 0.028 0.003 TRP E 159 HIS 0.008 0.002 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00790 (37124) covalent geometry : angle 0.73905 (50372) hydrogen bonds : bond 0.05888 ( 1549) hydrogen bonds : angle 5.65605 ( 4203) metal coordination : bond 0.00788 ( 40) metal coordination : angle 1.95121 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 331 time to evaluate : 1.550 Fit side-chains REVERT: A 46 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7369 (ttm-80) REVERT: A 131 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: A 175 MET cc_start: 0.7899 (mmm) cc_final: 0.7153 (mmm) REVERT: A 236 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8635 (tm-30) REVERT: A 278 ASN cc_start: 0.8296 (p0) cc_final: 0.8049 (p0) REVERT: A 394 ARG cc_start: 0.8629 (ttm110) cc_final: 0.8405 (ttm170) REVERT: A 692 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8057 (pp20) REVERT: A 768 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: A 2100 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6851 (mmtp) REVERT: C 46 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7360 (ttm-80) REVERT: C 131 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7760 (mm-30) REVERT: C 175 MET cc_start: 0.7942 (mmm) cc_final: 0.7193 (mmm) REVERT: C 236 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8629 (tm-30) REVERT: C 278 ASN cc_start: 0.8320 (p0) cc_final: 0.8054 (p0) REVERT: C 394 ARG cc_start: 0.8638 (ttm110) cc_final: 0.8418 (ttm170) REVERT: C 692 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8058 (pp20) REVERT: C 768 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: E 46 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7401 (ttm-80) REVERT: E 131 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: E 175 MET cc_start: 0.7942 (mmm) cc_final: 0.7193 (mmm) REVERT: E 236 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8623 (tm-30) REVERT: E 278 ASN cc_start: 0.8287 (p0) cc_final: 0.8041 (p0) REVERT: E 394 ARG cc_start: 0.8632 (ttm110) cc_final: 0.8407 (ttm170) REVERT: E 692 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8048 (pp20) REVERT: E 768 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: E 2100 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6860 (mmtp) REVERT: G 46 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7420 (ttm-80) REVERT: G 131 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7754 (mm-30) REVERT: G 175 MET cc_start: 0.7934 (mmm) cc_final: 0.7170 (mmm) REVERT: G 236 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8636 (tm-30) REVERT: G 278 ASN cc_start: 0.8294 (p0) cc_final: 0.8047 (p0) REVERT: G 394 ARG cc_start: 0.8633 (ttm110) cc_final: 0.8407 (ttm170) REVERT: G 692 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8054 (pp20) REVERT: G 768 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7584 (mm-30) outliers start: 129 outliers final: 44 residues processed: 433 average time/residue: 0.8675 time to fit residues: 443.1667 Evaluate side-chains 384 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 322 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 543 GLN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 1057 ASP Chi-restraints excluded: chain C residue 2100 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 734 ASN Chi-restraints excluded: chain E residue 768 GLU Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 1057 ASP Chi-restraints excluded: chain E residue 1060 GLU Chi-restraints excluded: chain E residue 2100 LYS Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 734 ASN Chi-restraints excluded: chain G residue 768 GLU Chi-restraints excluded: chain G residue 831 CYS Chi-restraints excluded: chain G residue 1057 ASP Chi-restraints excluded: chain G residue 2100 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 185 optimal weight: 0.9990 chunk 271 optimal weight: 0.5980 chunk 437 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 266 optimal weight: 2.9990 chunk 373 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 370 optimal weight: 0.6980 chunk 436 optimal weight: 0.9980 chunk 288 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 476 HIS A 775 GLN A 921 ASN C 248 ASN C 475 GLN C 665 GLN C 775 GLN C 921 ASN E 248 ASN E 475 GLN E 665 GLN E 775 GLN E 921 ASN G 248 ASN G 475 GLN G 476 HIS ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104533 restraints weight = 36606.582| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.42 r_work: 0.2978 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37164 Z= 0.135 Angle : 0.587 13.544 50408 Z= 0.312 Chirality : 0.045 0.156 5464 Planarity : 0.004 0.039 6516 Dihedral : 6.109 40.909 4856 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.60 % Allowed : 15.62 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.95 (0.12), residues: 4500 helix: 1.28 (0.16), residues: 1140 sheet: -0.72 (0.15), residues: 1108 loop : -1.61 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 677 TYR 0.016 0.001 TYR E 406 PHE 0.018 0.001 PHE C 896 TRP 0.015 0.001 TRP G 777 HIS 0.003 0.001 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00296 (37124) covalent geometry : angle 0.58595 (50372) hydrogen bonds : bond 0.04173 ( 1549) hydrogen bonds : angle 5.28881 ( 4203) metal coordination : bond 0.00413 ( 40) metal coordination : angle 1.62908 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 347 time to evaluate : 1.472 Fit side-chains REVERT: A 46 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7170 (ttm-80) REVERT: A 48 ASP cc_start: 0.8033 (p0) cc_final: 0.7677 (p0) REVERT: A 111 ARG cc_start: 0.8073 (ttt-90) cc_final: 0.7356 (ttm170) REVERT: A 236 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8553 (tm130) REVERT: A 278 ASN cc_start: 0.8283 (p0) cc_final: 0.8027 (p0) REVERT: C 46 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7171 (ttm-80) REVERT: C 48 ASP cc_start: 0.8040 (p0) cc_final: 0.7680 (p0) REVERT: C 111 ARG cc_start: 0.8090 (ttt-90) cc_final: 0.7357 (ttm170) REVERT: C 236 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8556 (tm130) REVERT: C 278 ASN cc_start: 0.8291 (p0) cc_final: 0.8034 (p0) REVERT: E 46 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7170 (ttm-80) REVERT: E 48 ASP cc_start: 0.8043 (p0) cc_final: 0.7686 (p0) REVERT: E 236 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8550 (tm130) REVERT: E 278 ASN cc_start: 0.8294 (p0) cc_final: 0.8037 (p0) REVERT: G 48 ASP cc_start: 0.8018 (p0) cc_final: 0.7666 (p0) REVERT: G 236 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8550 (tm130) REVERT: G 278 ASN cc_start: 0.8284 (p0) cc_final: 0.8028 (p0) outliers start: 104 outliers final: 31 residues processed: 427 average time/residue: 0.8130 time to fit residues: 411.7333 Evaluate side-chains 351 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 317 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain C residue 1057 ASP Chi-restraints excluded: chain C residue 2100 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1057 ASP Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 831 CYS Chi-restraints excluded: chain G residue 1056 ASN Chi-restraints excluded: chain G residue 1057 ASP Chi-restraints excluded: chain G residue 2100 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 417 optimal weight: 5.9990 chunk 447 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 321 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 442 optimal weight: 0.0980 chunk 419 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 475 GLN A 476 HIS A 775 GLN A 921 ASN A 996 ASN C 248 ASN ** C 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN C 921 ASN E 248 ASN E 775 GLN E 921 ASN G 248 ASN G 476 HIS ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103775 restraints weight = 36462.276| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.42 r_work: 0.2994 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37164 Z= 0.151 Angle : 0.590 12.359 50408 Z= 0.313 Chirality : 0.046 0.163 5464 Planarity : 0.004 0.035 6516 Dihedral : 6.050 42.042 4856 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.95 % Allowed : 15.68 % Favored : 81.38 % 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: -1.02 (0.12), residues: 4500 helix: 1.21 (0.15), residues: 1164 sheet: -0.73 (0.14), residues: 1132 loop : -1.70 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.018 0.002 TYR G 406 PHE 0.017 0.002 PHE C 896 TRP 0.016 0.001 TRP A 159 HIS 0.004 0.001 HIS C 952 Details of bonding type rmsd covalent geometry : bond 0.00339 (37124) covalent geometry : angle 0.58857 (50372) hydrogen bonds : bond 0.04280 ( 1549) hydrogen bonds : angle 5.25938 ( 4203) metal coordination : bond 0.00526 ( 40) metal coordination : angle 1.63874 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 340 time to evaluate : 1.505 Fit side-chains REVERT: A 46 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7273 (ttm-80) REVERT: A 111 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7434 (ttm170) REVERT: A 236 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8557 (tm130) REVERT: A 278 ASN cc_start: 0.8213 (p0) cc_final: 0.7954 (p0) REVERT: A 768 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: A 2100 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6892 (mmtp) REVERT: C 46 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7287 (ttm-80) REVERT: C 111 ARG cc_start: 0.8107 (ttt-90) cc_final: 0.7434 (ttm170) REVERT: C 236 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8552 (tm130) REVERT: C 278 ASN cc_start: 0.8219 (p0) cc_final: 0.7958 (p0) REVERT: C 768 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: E 46 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7295 (ttm-80) REVERT: E 111 ARG cc_start: 0.8106 (ttt-90) cc_final: 0.7423 (ttm170) REVERT: E 236 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8551 (tm130) REVERT: E 278 ASN cc_start: 0.8212 (p0) cc_final: 0.7953 (p0) REVERT: E 768 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: E 2100 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6898 (mmtp) REVERT: G 46 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7262 (ttm-80) REVERT: G 111 ARG cc_start: 0.8114 (ttt-90) cc_final: 0.7436 (ttm170) REVERT: G 236 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8547 (tm130) REVERT: G 278 ASN cc_start: 0.8201 (p0) cc_final: 0.7939 (p0) REVERT: G 768 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7518 (mm-30) outliers start: 118 outliers final: 38 residues processed: 428 average time/residue: 0.7352 time to fit residues: 377.0764 Evaluate side-chains 367 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain C residue 1057 ASP Chi-restraints excluded: chain C residue 2100 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 768 GLU Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 1052 THR Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1057 ASP Chi-restraints excluded: chain E residue 1060 GLU Chi-restraints excluded: chain E residue 2100 LYS Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 768 GLU Chi-restraints excluded: chain G residue 831 CYS Chi-restraints excluded: chain G residue 1052 THR Chi-restraints excluded: chain G residue 1056 ASN Chi-restraints excluded: chain G residue 1057 ASP Chi-restraints excluded: chain G residue 2100 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 214 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 216 optimal weight: 0.5980 chunk 420 optimal weight: 4.9990 chunk 354 optimal weight: 0.5980 chunk 375 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 378 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 475 GLN A 521 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 921 ASN C 248 ASN C 475 GLN C 521 ASN C 775 GLN C 921 ASN C 996 ASN E 248 ASN E 475 GLN E 521 ASN E 775 GLN E 921 ASN E 996 ASN G 248 ASN G 475 GLN G 521 ASN ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN G 996 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105419 restraints weight = 36667.544| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.42 r_work: 0.2996 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37164 Z= 0.129 Angle : 0.571 11.511 50408 Z= 0.302 Chirality : 0.045 0.162 5464 Planarity : 0.004 0.033 6516 Dihedral : 5.897 43.032 4856 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.77 % Allowed : 16.12 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.12), residues: 4500 helix: 1.39 (0.16), residues: 1144 sheet: -0.73 (0.15), residues: 1132 loop : -1.58 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 677 TYR 0.015 0.001 TYR A 406 PHE 0.018 0.001 PHE E 896 TRP 0.015 0.001 TRP C 777 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00287 (37124) covalent geometry : angle 0.56938 (50372) hydrogen bonds : bond 0.03985 ( 1549) hydrogen bonds : angle 5.15121 ( 4203) metal coordination : bond 0.00506 ( 40) metal coordination : angle 1.60994 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 333 time to evaluate : 1.358 Fit side-chains REVERT: A 46 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7207 (ttm170) REVERT: A 114 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7521 (mptt) REVERT: A 236 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8546 (tm130) REVERT: A 278 ASN cc_start: 0.8214 (p0) cc_final: 0.7937 (p0) REVERT: A 378 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8686 (mmt90) REVERT: A 768 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: A 2100 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6739 (mmtp) REVERT: C 46 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7197 (ttm170) REVERT: C 111 ARG cc_start: 0.8035 (ttt-90) cc_final: 0.7369 (ttm170) REVERT: C 114 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7558 (mptt) REVERT: C 236 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8537 (tm130) REVERT: C 278 ASN cc_start: 0.8224 (p0) cc_final: 0.7947 (p0) REVERT: C 378 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8687 (mmt90) REVERT: C 768 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: E 46 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7181 (ttm170) REVERT: E 111 ARG cc_start: 0.8038 (ttt-90) cc_final: 0.7368 (ttm170) REVERT: E 114 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7560 (mptt) REVERT: E 236 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8539 (tm130) REVERT: E 278 ASN cc_start: 0.8216 (p0) cc_final: 0.7939 (p0) REVERT: E 378 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8681 (mmt90) REVERT: E 768 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: E 2100 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6816 (mmtp) REVERT: G 46 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7205 (ttm-80) REVERT: G 111 ARG cc_start: 0.8051 (ttt-90) cc_final: 0.7378 (ttm170) REVERT: G 114 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7549 (mptt) REVERT: G 236 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8530 (tm130) REVERT: G 278 ASN cc_start: 0.8216 (p0) cc_final: 0.7936 (p0) REVERT: G 378 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8681 (mmt90) REVERT: G 768 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7483 (mm-30) outliers start: 111 outliers final: 42 residues processed: 414 average time/residue: 0.8417 time to fit residues: 411.7408 Evaluate side-chains 385 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 768 GLU Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 1052 THR Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 2100 LYS Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 378 ARG Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 768 GLU Chi-restraints excluded: chain G residue 831 CYS Chi-restraints excluded: chain G residue 1052 THR Chi-restraints excluded: chain G residue 1056 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 71 optimal weight: 5.9990 chunk 225 optimal weight: 0.0980 chunk 213 optimal weight: 1.9990 chunk 330 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 348 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 411 optimal weight: 0.7980 chunk 273 optimal weight: 0.0030 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 248 ASN A 475 GLN A 476 HIS ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 921 ASN C 127 ASN C 248 ASN C 475 GLN C 665 GLN C 775 GLN C 921 ASN E 127 ASN E 248 ASN E 475 GLN E 665 GLN E 775 GLN E 921 ASN G 127 ASN G 248 ASN G 475 GLN G 476 HIS ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108595 restraints weight = 36894.860| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.37 r_work: 0.3034 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 37164 Z= 0.114 Angle : 0.549 10.883 50408 Z= 0.289 Chirality : 0.044 0.159 5464 Planarity : 0.003 0.032 6516 Dihedral : 5.673 40.465 4856 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.60 % Allowed : 16.98 % 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: -0.78 (0.12), residues: 4500 helix: 1.49 (0.16), residues: 1144 sheet: -0.66 (0.15), residues: 1124 loop : -1.53 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 677 TYR 0.013 0.001 TYR C 627 PHE 0.018 0.001 PHE A 896 TRP 0.015 0.001 TRP E 777 HIS 0.002 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00249 (37124) covalent geometry : angle 0.54737 (50372) hydrogen bonds : bond 0.03693 ( 1549) hydrogen bonds : angle 5.04149 ( 4203) metal coordination : bond 0.00521 ( 40) metal coordination : angle 1.69582 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 352 time to evaluate : 1.235 Fit side-chains REVERT: A 46 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7224 (ttm170) REVERT: A 111 ARG cc_start: 0.8062 (ttt-90) cc_final: 0.7339 (ttm170) REVERT: A 278 ASN cc_start: 0.8191 (p0) cc_final: 0.7979 (p0) REVERT: A 354 ASN cc_start: 0.8321 (t0) cc_final: 0.7964 (t0) REVERT: A 2100 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6766 (mmtp) REVERT: C 46 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7220 (ttm170) REVERT: C 111 ARG cc_start: 0.8023 (ttt-90) cc_final: 0.7369 (ttm170) REVERT: C 176 PHE cc_start: 0.8434 (m-80) cc_final: 0.8223 (m-80) REVERT: C 278 ASN cc_start: 0.8195 (p0) cc_final: 0.7979 (p0) REVERT: E 46 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7220 (ttm170) REVERT: E 111 ARG cc_start: 0.8002 (ttt-90) cc_final: 0.7335 (ttm170) REVERT: E 176 PHE cc_start: 0.8436 (m-80) cc_final: 0.8225 (m-80) REVERT: E 278 ASN cc_start: 0.8187 (p0) cc_final: 0.7973 (p0) REVERT: E 2100 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6737 (mmtp) REVERT: G 46 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7158 (ttm-80) REVERT: G 111 ARG cc_start: 0.8037 (ttt-90) cc_final: 0.7369 (ttm170) REVERT: G 278 ASN cc_start: 0.8202 (p0) cc_final: 0.7905 (p0) outliers start: 104 outliers final: 41 residues processed: 429 average time/residue: 0.7909 time to fit residues: 403.9712 Evaluate side-chains 376 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 329 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 810 ASP Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 1052 THR Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 2100 LYS Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 810 ASP Chi-restraints excluded: chain G residue 831 CYS Chi-restraints excluded: chain G residue 1052 THR Chi-restraints excluded: chain G residue 1056 ASN Chi-restraints excluded: chain G residue 1060 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 414 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 chunk 417 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 415 optimal weight: 0.3980 chunk 132 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 366 optimal weight: 0.5980 chunk 230 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 236 GLN A 248 ASN A 476 HIS ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 921 ASN C 127 ASN C 236 GLN C 248 ASN C 775 GLN C 921 ASN E 127 ASN E 236 GLN E 248 ASN E 775 GLN E 921 ASN G 127 ASN G 236 GLN G 248 ASN G 476 HIS ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104506 restraints weight = 36641.595| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.42 r_work: 0.2980 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37164 Z= 0.175 Angle : 0.597 10.228 50408 Z= 0.315 Chirality : 0.046 0.163 5464 Planarity : 0.004 0.040 6516 Dihedral : 5.860 40.881 4856 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.12 % Allowed : 16.98 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.12), residues: 4500 helix: 1.32 (0.16), residues: 1164 sheet: -0.69 (0.15), residues: 1132 loop : -1.61 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 677 TYR 0.017 0.002 TYR C 406 PHE 0.017 0.002 PHE C 896 TRP 0.016 0.002 TRP C 777 HIS 0.005 0.001 HIS C 952 Details of bonding type rmsd covalent geometry : bond 0.00402 (37124) covalent geometry : angle 0.59550 (50372) hydrogen bonds : bond 0.04283 ( 1549) hydrogen bonds : angle 5.14567 ( 4203) metal coordination : bond 0.00601 ( 40) metal coordination : angle 1.66350 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 324 time to evaluate : 1.380 Fit side-chains REVERT: A 46 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7248 (ttm170) REVERT: A 222 LYS cc_start: 0.8644 (mtmp) cc_final: 0.8437 (mtmp) REVERT: A 278 ASN cc_start: 0.8202 (p0) cc_final: 0.7899 (p0) REVERT: A 354 ASN cc_start: 0.8389 (t0) cc_final: 0.8039 (t0) REVERT: A 2100 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6781 (mmtp) REVERT: C 46 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7235 (ttm170) REVERT: C 176 PHE cc_start: 0.8460 (m-80) cc_final: 0.8247 (m-80) REVERT: C 222 LYS cc_start: 0.8655 (mtmp) cc_final: 0.8449 (mtmp) REVERT: C 278 ASN cc_start: 0.8207 (p0) cc_final: 0.7902 (p0) REVERT: E 46 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7236 (ttm170) REVERT: E 176 PHE cc_start: 0.8458 (m-80) cc_final: 0.8245 (m-80) REVERT: E 222 LYS cc_start: 0.8651 (mtmp) cc_final: 0.8445 (mtmp) REVERT: E 278 ASN cc_start: 0.8185 (p0) cc_final: 0.7883 (p0) REVERT: E 2100 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6706 (mmtp) REVERT: G 46 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7180 (ttm-80) REVERT: G 222 LYS cc_start: 0.8643 (mtmp) cc_final: 0.8438 (mtmp) REVERT: G 278 ASN cc_start: 0.8219 (p0) cc_final: 0.7924 (p0) outliers start: 85 outliers final: 46 residues processed: 379 average time/residue: 0.7733 time to fit residues: 349.6571 Evaluate side-chains 375 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain C residue 1060 GLU Chi-restraints excluded: chain C residue 2100 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 1052 THR Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 2100 LYS Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 831 CYS Chi-restraints excluded: chain G residue 1052 THR Chi-restraints excluded: chain G residue 1056 ASN Chi-restraints excluded: chain G residue 1060 GLU Chi-restraints excluded: chain G residue 2100 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 355 optimal weight: 1.9990 chunk 217 optimal weight: 0.0030 chunk 25 optimal weight: 1.9990 chunk 381 optimal weight: 0.9990 chunk 393 optimal weight: 4.9990 chunk 337 optimal weight: 0.0070 chunk 168 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 447 optimal weight: 0.0370 chunk 191 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 0.2686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 248 ASN A 775 GLN A 921 ASN C 127 ASN C 248 ASN C 476 HIS C 775 GLN C 921 ASN E 127 ASN E 248 ASN E 476 HIS E 775 GLN E 921 ASN G 127 ASN G 248 ASN ** G 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110224 restraints weight = 37170.821| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.43 r_work: 0.3122 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 37164 Z= 0.104 Angle : 0.542 9.911 50408 Z= 0.285 Chirality : 0.044 0.171 5464 Planarity : 0.003 0.034 6516 Dihedral : 5.482 40.892 4856 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.90 % Allowed : 17.50 % Favored : 80.60 % 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: -0.68 (0.13), residues: 4500 helix: 1.53 (0.16), residues: 1144 sheet: -0.60 (0.15), residues: 1096 loop : -1.43 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 677 TYR 0.012 0.001 TYR C1058 PHE 0.017 0.001 PHE A 531 TRP 0.014 0.001 TRP E 845 HIS 0.003 0.001 HIS A 726 Details of bonding type rmsd covalent geometry : bond 0.00226 (37124) covalent geometry : angle 0.54060 (50372) hydrogen bonds : bond 0.03400 ( 1549) hydrogen bonds : angle 4.94287 ( 4203) metal coordination : bond 0.00453 ( 40) metal coordination : angle 1.73949 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 353 time to evaluate : 1.390 Fit side-chains REVERT: A 236 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8328 (tm130) REVERT: A 240 ASP cc_start: 0.8192 (m-30) cc_final: 0.7935 (m-30) REVERT: A 923 MET cc_start: 0.9223 (mtp) cc_final: 0.8918 (mtp) REVERT: C 176 PHE cc_start: 0.8333 (m-80) cc_final: 0.8113 (m-80) REVERT: C 278 ASN cc_start: 0.8062 (p0) cc_final: 0.7860 (p0) REVERT: C 923 MET cc_start: 0.9221 (mtp) cc_final: 0.8916 (mtp) REVERT: E 176 PHE cc_start: 0.8346 (m-80) cc_final: 0.8128 (m-80) REVERT: E 236 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8339 (tm130) REVERT: E 240 ASP cc_start: 0.8165 (m-30) cc_final: 0.7915 (m-30) REVERT: E 923 MET cc_start: 0.9219 (mtp) cc_final: 0.8908 (mtp) REVERT: G 192 TYR cc_start: 0.8211 (m-80) cc_final: 0.7940 (m-80) REVERT: G 923 MET cc_start: 0.9236 (mtp) cc_final: 0.8904 (mtp) outliers start: 76 outliers final: 42 residues processed: 405 average time/residue: 0.7395 time to fit residues: 358.4569 Evaluate side-chains 377 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 335 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 2084 VAL Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 810 ASP Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 1052 THR Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 810 ASP Chi-restraints excluded: chain G residue 831 CYS Chi-restraints excluded: chain G residue 1052 THR Chi-restraints excluded: chain G residue 1056 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 128 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 333 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 359 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 248 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 921 ASN C 127 ASN C 236 GLN C 248 ASN C 476 HIS C 665 GLN C 775 GLN C 921 ASN E 127 ASN E 248 ASN E 476 HIS E 665 GLN E 775 GLN E 921 ASN G 127 ASN G 236 GLN G 248 ASN G 665 GLN ** G 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102056 restraints weight = 36610.822| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.37 r_work: 0.2926 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 37164 Z= 0.270 Angle : 0.691 10.486 50408 Z= 0.366 Chirality : 0.050 0.188 5464 Planarity : 0.005 0.059 6516 Dihedral : 6.214 40.584 4856 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.95 % Allowed : 18.82 % Favored : 80.22 % 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: -1.01 (0.12), residues: 4500 helix: 1.14 (0.15), residues: 1164 sheet: -0.69 (0.14), residues: 1120 loop : -1.68 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 191 TYR 0.021 0.003 TYR C 406 PHE 0.018 0.002 PHE C 896 TRP 0.020 0.002 TRP A 159 HIS 0.006 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00624 (37124) covalent geometry : angle 0.68879 (50372) hydrogen bonds : bond 0.05172 ( 1549) hydrogen bonds : angle 5.39416 ( 4203) metal coordination : bond 0.00747 ( 40) metal coordination : angle 1.95873 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9000 Ramachandran restraints generated. 4500 Oldfield, 0 Emsley, 4500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 322 time to evaluate : 1.350 Fit side-chains REVERT: A 2100 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6686 (mmtp) REVERT: C 176 PHE cc_start: 0.8492 (m-80) cc_final: 0.8288 (m-80) REVERT: C 278 ASN cc_start: 0.8210 (p0) cc_final: 0.7912 (p0) outliers start: 38 outliers final: 30 residues processed: 354 average time/residue: 0.8306 time to fit residues: 348.5590 Evaluate side-chains 340 residues out of total 4004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 2100 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 810 ASP Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 810 ASP Chi-restraints excluded: chain E residue 831 CYS Chi-restraints excluded: chain E residue 1052 THR Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain G residue 810 ASP Chi-restraints excluded: chain G residue 831 CYS Chi-restraints excluded: chain G residue 1052 THR Chi-restraints excluded: chain G residue 1056 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 26 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 419 optimal weight: 0.9980 chunk 246 optimal weight: 0.7980 chunk 388 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 248 ASN A 354 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A 921 ASN C 248 ASN C 521 ASN C 665 GLN C 775 GLN C 921 ASN E 236 GLN E 248 ASN E 354 ASN E 665 GLN E 775 GLN E 921 ASN G 248 ASN G 354 ASN G 665 GLN ** G 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 GLN G 921 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105384 restraints weight = 36613.428| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.36 r_work: 0.3005 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37164 Z= 0.158 Angle : 0.607 10.173 50408 Z= 0.321 Chirality : 0.046 0.159 5464 Planarity : 0.004 0.033 6516 Dihedral : 5.970 39.892 4856 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.07 % Allowed : 18.70 % Favored : 80.22 % 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: -0.97 (0.12), residues: 4500 helix: 1.22 (0.15), residues: 1164 sheet: -0.72 (0.14), residues: 1120 loop : -1.64 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 191 TYR 0.022 0.002 TYR E 406 PHE 0.018 0.002 PHE C 896 TRP 0.016 0.001 TRP G 159 HIS 0.004 0.001 HIS G 952 Details of bonding type rmsd covalent geometry : bond 0.00358 (37124) covalent geometry : angle 0.60602 (50372) hydrogen bonds : bond 0.04286 ( 1549) hydrogen bonds : angle 5.23574 ( 4203) metal coordination : bond 0.00539 ( 40) metal coordination : angle 1.68933 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14623.47 seconds wall clock time: 250 minutes 2.72 seconds (15002.72 seconds total)