Starting phenix.real_space_refine on Fri Mar 6 20:16:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mka_23888/03_2026/7mka_23888.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mka_23888/03_2026/7mka_23888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mka_23888/03_2026/7mka_23888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mka_23888/03_2026/7mka_23888.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mka_23888/03_2026/7mka_23888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mka_23888/03_2026/7mka_23888.map" } resolution = 3.54 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 871 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 95 5.49 5 Mg 2 5.21 5 S 181 5.16 5 C 20739 2.51 5 N 5818 2.21 5 O 6541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 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: 33384 Number of models: 1 Model: "" Number of chains: 21 Chain: "N" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 798 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "O" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 821 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "a" Number of atoms: 11189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 11189 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 65, 'TRANS': 1355} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "b" Number of atoms: 9197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9197 Classifications: {'peptide': 1160} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 5} Link IDs: {'CIS': 12, 'PCIS': 2, 'PTRANS': 49, 'TRANS': 1096} Chain breaks: 8 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "c" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "d" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1331 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "f" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "g" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "h" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Chain: "i" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "j" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "k" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "l" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "r" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 11} Chain: "a" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2459 SG CYS a 110 118.522 92.122 101.095 1.00216.77 S ATOM 2764 SG CYS a 148 118.359 90.034 104.145 1.00265.00 S ATOM 2902 SG CYS a 167 118.716 93.328 103.507 1.00271.97 S ATOM 2130 SG CYS a 67 101.242 103.924 55.935 1.00242.80 S ATOM 2152 SG CYS a 70 102.931 104.297 54.678 1.00263.01 S ATOM 21530 SG CYS b1163 112.630 92.713 62.884 1.00771.81 S ATOM 21548 SG CYS b1166 111.149 94.815 65.698 1.00731.01 S ATOM 21673 SG CYS b1182 111.818 96.553 62.930 1.00879.94 S ATOM 21692 SG CYS b1185 113.979 94.998 65.968 1.00908.11 S ATOM 22652 SG CYS c 86 44.460 94.148 18.041 1.00652.87 S ATOM 22669 SG CYS c 88 46.148 96.993 19.675 1.00684.17 S ATOM 22702 SG CYS c 92 42.913 97.678 17.810 1.00633.55 S ATOM 22725 SG CYS c 95 43.260 95.914 21.310 1.00603.63 S ATOM 30351 SG CYS i 7 60.869 90.821 144.402 1.00606.34 S ATOM 30376 SG CYS i 10 62.575 93.140 141.777 1.00604.81 S ATOM 30542 SG CYS i 29 64.284 89.954 142.971 1.00592.83 S ATOM 30566 SG CYS i 32 63.719 92.765 145.451 1.00615.85 S ATOM 30893 SG CYS i 75 26.711 66.210 121.024 1.00999.99 S ATOM 30915 SG CYS i 78 25.148 68.332 122.861 1.00999.99 S ATOM 31131 SG CYS i 103 26.638 69.766 119.530 1.00999.99 S ATOM 31151 SG CYS i 106 28.924 69.043 122.571 1.00999.99 S ATOM 31279 SG CYS j 7 30.918 83.427 48.516 1.00416.77 S ATOM 31302 SG CYS j 10 29.679 82.471 45.179 1.00474.02 S ATOM 31582 SG CYS j 45 28.733 79.949 47.886 1.00511.53 S ATOM 31588 SG CYS j 46 27.217 83.208 47.010 1.00497.40 S ATOM 32732 SG CYS l 31 43.970 125.547 56.097 1.00283.35 S ATOM 32752 SG CYS l 34 40.854 127.102 55.926 1.00331.71 S ATOM 32856 SG CYS l 48 44.100 129.192 55.782 1.00280.24 S ATOM 32879 SG CYS l 51 42.245 127.713 59.026 1.00298.71 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN a1801 " occ=0.95 Time building chain proxies: 7.69, per 1000 atoms: 0.23 Number of scatterers: 33384 At special positions: 0 Unit cell: (170.64, 163.08, 164.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 181 16.00 P 95 15.00 Mg 2 11.99 O 6541 8.00 N 5818 7.00 C 20739 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: 3.28 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a1801 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 167 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 148 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 110 " pdb=" ZN a1802 " pdb="ZN ZN a1802 " - pdb=" SG CYS a 67 " pdb="ZN ZN a1802 " - pdb=" SG CYS a 70 " pdb="ZN ZN a1802 " - pdb=" NE2 HIS a 80 " pdb=" ZN b1301 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1166 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1185 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1182 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1163 " pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 88 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 95 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 92 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 86 " pdb=" ZN i 201 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 32 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 29 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 7 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 10 " pdb=" ZN i 202 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 78 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 75 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 106 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 103 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 10 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 46 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 45 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 7 " pdb=" ZN l 101 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 34 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 31 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 48 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 51 " Number of angles added : 36 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7440 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 42 sheets defined 37.3% alpha, 14.9% beta 29 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 4.61 Creating SS restraints... Processing helix chain 'a' and resid 23 through 31 Processing helix chain 'a' and resid 92 through 95 Processing helix chain 'a' and resid 96 through 105 Processing helix chain 'a' and resid 120 through 128 Processing helix chain 'a' and resid 132 through 142 Processing helix chain 'a' and resid 191 through 195 Processing helix chain 'a' and resid 203 through 214 Processing helix chain 'a' and resid 215 through 222 removed outlier: 3.715A pdb=" N PHE a 219 " --> pdb=" O SER a 215 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR a 220 " --> pdb=" O VAL a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 235 removed outlier: 3.581A pdb=" N ILE a 235 " --> pdb=" O GLU a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 243 through 247 removed outlier: 3.551A pdb=" N VAL a 246 " --> pdb=" O PRO a 243 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 282 removed outlier: 3.528A pdb=" N PHE a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 288 through 305 Processing helix chain 'a' and resid 324 through 330 Processing helix chain 'a' and resid 368 through 374 Processing helix chain 'a' and resid 384 through 395 Processing helix chain 'a' and resid 471 through 473 No H-bonds generated for 'chain 'a' and resid 471 through 473' Processing helix chain 'a' and resid 474 through 479 removed outlier: 3.633A pdb=" N TYR a 478 " --> pdb=" O VAL a 474 " (cutoff:3.500A) Processing helix chain 'a' and resid 494 through 502 Processing helix chain 'a' and resid 506 through 510 Processing helix chain 'a' and resid 524 through 535 Processing helix chain 'a' and resid 542 through 553 Processing helix chain 'a' and resid 573 through 581 removed outlier: 3.929A pdb=" N VAL a 580 " --> pdb=" O GLN a 576 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA a 581 " --> pdb=" O ILE a 577 " (cutoff:3.500A) Processing helix chain 'a' and resid 618 through 623 Processing helix chain 'a' and resid 628 through 637 Processing helix chain 'a' and resid 640 through 661 removed outlier: 3.933A pdb=" N LYS a 644 " --> pdb=" O GLN a 640 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE a 655 " --> pdb=" O LYS a 651 " (cutoff:3.500A) Processing helix chain 'a' and resid 665 through 669 Processing helix chain 'a' and resid 672 through 699 Processing helix chain 'a' and resid 709 through 737 Processing helix chain 'a' and resid 741 through 749 removed outlier: 3.903A pdb=" N GLN a 745 " --> pdb=" O ASN a 741 " (cutoff:3.500A) Processing helix chain 'a' and resid 754 through 763 Processing helix chain 'a' and resid 809 through 843 removed outlier: 4.724A pdb=" N ALA a 832 " --> pdb=" O ALA a 828 " (cutoff:3.500A) Processing helix chain 'a' and resid 867 through 871 Processing helix chain 'a' and resid 889 through 898 Processing helix chain 'a' and resid 909 through 913 Processing helix chain 'a' and resid 922 through 947 Processing helix chain 'a' and resid 960 through 970 Processing helix chain 'a' and resid 982 through 997 removed outlier: 4.200A pdb=" N LYS a 991 " --> pdb=" O VAL a 987 " (cutoff:3.500A) Processing helix chain 'a' and resid 1004 through 1015 removed outlier: 3.627A pdb=" N GLN a1008 " --> pdb=" O ASN a1004 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL a1015 " --> pdb=" O GLN a1011 " (cutoff:3.500A) Processing helix chain 'a' and resid 1015 through 1026 Processing helix chain 'a' and resid 1027 through 1034 Processing helix chain 'a' and resid 1038 through 1056 Processing helix chain 'a' and resid 1063 through 1078 Proline residue: a1075 - end of helix removed outlier: 3.902A pdb=" N GLN a1078 " --> pdb=" O GLU a1074 " (cutoff:3.500A) Processing helix chain 'a' and resid 1096 through 1106 Processing helix chain 'a' and resid 1127 through 1139 Processing helix chain 'a' and resid 1142 through 1146 removed outlier: 3.568A pdb=" N VAL a1146 " --> pdb=" O THR a1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1142 through 1146' Processing helix chain 'a' and resid 1167 through 1173 Processing helix chain 'a' and resid 1198 through 1205 Processing helix chain 'a' and resid 1208 through 1220 removed outlier: 3.746A pdb=" N PHE a1220 " --> pdb=" O ILE a1216 " (cutoff:3.500A) Processing helix chain 'a' and resid 1255 through 1269 removed outlier: 3.511A pdb=" N MET a1259 " --> pdb=" O GLU a1255 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU a1269 " --> pdb=" O ASN a1265 " (cutoff:3.500A) Processing helix chain 'a' and resid 1315 through 1319 Processing helix chain 'a' and resid 1331 through 1339 Processing helix chain 'a' and resid 1340 through 1358 Processing helix chain 'a' and resid 1364 through 1377 removed outlier: 4.114A pdb=" N MET a1368 " --> pdb=" O ASN a1364 " (cutoff:3.500A) Processing helix chain 'a' and resid 1395 through 1401 removed outlier: 3.823A pdb=" N ARG a1399 " --> pdb=" O GLY a1395 " (cutoff:3.500A) Processing helix chain 'a' and resid 1406 through 1416 Processing helix chain 'a' and resid 1423 through 1431 Processing helix chain 'a' and resid 1436 through 1441 removed outlier: 4.049A pdb=" N PHE a1441 " --> pdb=" O THR a1438 " (cutoff:3.500A) Processing helix chain 'a' and resid 1447 through 1453 Processing helix chain 'b' and resid 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 through 29' Processing helix chain 'b' and resid 30 through 42 removed outlier: 3.872A pdb=" N ILE b 34 " --> pdb=" O SER b 30 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER b 35 " --> pdb=" O TRP b 31 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 57 removed outlier: 3.629A pdb=" N PHE b 51 " --> pdb=" O GLN b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 66 removed outlier: 4.153A pdb=" N ASP b 66 " --> pdb=" O ILE b 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 121 Processing helix chain 'b' and resid 179 through 184 Processing helix chain 'b' and resid 185 through 192 Processing helix chain 'b' and resid 246 through 250 removed outlier: 3.515A pdb=" N PHE b 250 " --> pdb=" O GLY b 247 " (cutoff:3.500A) Processing helix chain 'b' and resid 282 through 290 Processing helix chain 'b' and resid 293 through 302 removed outlier: 3.627A pdb=" N ILE b 297 " --> pdb=" O PRO b 293 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 321 Proline residue: b 316 - end of helix removed outlier: 3.583A pdb=" N GLY b 321 " --> pdb=" O CYS b 317 " (cutoff:3.500A) Processing helix chain 'b' and resid 322 through 324 No H-bonds generated for 'chain 'b' and resid 322 through 324' Processing helix chain 'b' and resid 326 through 333 Processing helix chain 'b' and resid 348 through 359 Processing helix chain 'b' and resid 370 through 390 Processing helix chain 'b' and resid 408 through 430 removed outlier: 3.900A pdb=" N LEU b 416 " --> pdb=" O LEU b 412 " (cutoff:3.500A) Processing helix chain 'b' and resid 444 through 464 removed outlier: 4.250A pdb=" N ILE b 448 " --> pdb=" O MET b 444 " (cutoff:3.500A) Processing helix chain 'b' and resid 487 through 496 removed outlier: 3.878A pdb=" N ARG b 496 " --> pdb=" O LEU b 492 " (cutoff:3.500A) Processing helix chain 'b' and resid 515 through 519 Processing helix chain 'b' and resid 551 through 561 removed outlier: 3.825A pdb=" N ILE b 555 " --> pdb=" O PRO b 551 " (cutoff:3.500A) Processing helix chain 'b' and resid 565 through 569 Processing helix chain 'b' and resid 592 through 606 removed outlier: 3.943A pdb=" N LEU b 596 " --> pdb=" O ASN b 592 " (cutoff:3.500A) Processing helix chain 'b' and resid 654 through 668 removed outlier: 3.629A pdb=" N ILE b 658 " --> pdb=" O ARG b 654 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP b 668 " --> pdb=" O THR b 664 " (cutoff:3.500A) Processing helix chain 'b' and resid 680 through 688 removed outlier: 3.523A pdb=" N GLY b 688 " --> pdb=" O LEU b 684 " (cutoff:3.500A) Processing helix chain 'b' and resid 695 through 699 removed outlier: 4.143A pdb=" N GLU b 699 " --> pdb=" O ALA b 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 695 through 699' Processing helix chain 'b' and resid 744 through 749 Processing helix chain 'b' and resid 750 through 756 removed outlier: 4.071A pdb=" N ILE b 755 " --> pdb=" O VAL b 751 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE b 756 " --> pdb=" O ALA b 752 " (cutoff:3.500A) Processing helix chain 'b' and resid 758 through 762 Processing helix chain 'b' and resid 763 through 775 removed outlier: 4.131A pdb=" N LYS b 775 " --> pdb=" O SER b 771 " (cutoff:3.500A) Processing helix chain 'b' and resid 807 through 812 Processing helix chain 'b' and resid 843 through 849 Processing helix chain 'b' and resid 889 through 893 removed outlier: 3.585A pdb=" N LYS b 892 " --> pdb=" O THR b 889 " (cutoff:3.500A) Processing helix chain 'b' and resid 995 through 999 Processing helix chain 'b' and resid 1014 through 1017 Processing helix chain 'b' and resid 1023 through 1039 Processing helix chain 'b' and resid 1051 through 1063 removed outlier: 3.517A pdb=" N ILE b1055 " --> pdb=" O THR b1051 " (cutoff:3.500A) Processing helix chain 'b' and resid 1099 through 1103 Processing helix chain 'b' and resid 1131 through 1142 Processing helix chain 'b' and resid 1143 through 1153 Processing helix chain 'b' and resid 1197 through 1210 Processing helix chain 'c' and resid 26 through 40 Processing helix chain 'c' and resid 59 through 68 Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'c' and resid 92 through 96 removed outlier: 3.696A pdb=" N SER c 96 " --> pdb=" O ASP c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 114 through 118 removed outlier: 3.525A pdb=" N LEU c 118 " --> pdb=" O SER c 115 " (cutoff:3.500A) Processing helix chain 'c' and resid 167 through 171 Processing helix chain 'c' and resid 204 through 209 Processing helix chain 'c' and resid 239 through 266 Processing helix chain 'd' and resid 51 through 75 removed outlier: 3.582A pdb=" N ALA d 55 " --> pdb=" O ASN d 51 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG d 56 " --> pdb=" O LEU d 52 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU d 57 " --> pdb=" O SER d 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS d 75 " --> pdb=" O LYS d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 134 removed outlier: 4.145A pdb=" N THR d 133 " --> pdb=" O LEU d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 138 through 152 removed outlier: 4.306A pdb=" N ASN d 150 " --> pdb=" O GLN d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 171 removed outlier: 3.842A pdb=" N SER d 169 " --> pdb=" O GLN d 165 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR d 170 " --> pdb=" O LEU d 166 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 179 removed outlier: 4.060A pdb=" N VAL d 177 " --> pdb=" O HIS d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 180 through 183 removed outlier: 4.012A pdb=" N LEU d 183 " --> pdb=" O LEU d 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 180 through 183' Processing helix chain 'd' and resid 187 through 195 removed outlier: 4.166A pdb=" N ALA d 191 " --> pdb=" O THR d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 202 removed outlier: 4.044A pdb=" N ASN d 199 " --> pdb=" O ILE d 195 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE d 202 " --> pdb=" O LEU d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 216 removed outlier: 4.588A pdb=" N GLU d 213 " --> pdb=" O ARG d 209 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU d 214 " --> pdb=" O ILE d 210 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN d 216 " --> pdb=" O LYS d 212 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 26 removed outlier: 4.389A pdb=" N ARG e 7 " --> pdb=" O GLN e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 36 removed outlier: 3.540A pdb=" N VAL e 35 " --> pdb=" O THR e 31 " (cutoff:3.500A) Processing helix chain 'e' and resid 38 through 47 Processing helix chain 'e' and resid 65 through 72 Processing helix chain 'e' and resid 89 through 104 Processing helix chain 'e' and resid 117 through 122 Processing helix chain 'e' and resid 157 through 169 Processing helix chain 'e' and resid 182 through 189 Processing helix chain 'f' and resid 86 through 103 Processing helix chain 'f' and resid 116 through 128 Processing helix chain 'g' and resid 14 through 18 Processing helix chain 'g' and resid 21 through 35 Processing helix chain 'i' and resid 61 through 65 removed outlier: 3.710A pdb=" N ASP i 65 " --> pdb=" O ILE i 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 17 through 28 Processing helix chain 'j' and resid 31 through 40 Processing helix chain 'j' and resid 43 through 52 removed outlier: 3.813A pdb=" N ARG j 47 " --> pdb=" O ARG j 43 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET j 49 " --> pdb=" O CYS j 45 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE j 50 " --> pdb=" O CYS j 46 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 62 Processing helix chain 'k' and resid 6 through 10 removed outlier: 3.548A pdb=" N LEU k 9 " --> pdb=" O ARG k 6 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 52 removed outlier: 3.684A pdb=" N GLY k 43 " --> pdb=" O ASP k 39 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU k 45 " --> pdb=" O THR k 41 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN k 52 " --> pdb=" O ALA k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 112 Processing sheet with id=AA1, first strand: chain 'a' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'a' and resid 82 through 83 removed outlier: 3.769A pdb=" N GLY a 82 " --> pdb=" O VAL a 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'a' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'a' and resid 343 through 344 Processing sheet with id=AA6, first strand: chain 'a' and resid 455 through 458 removed outlier: 3.559A pdb=" N MET a 487 " --> pdb=" O THR a 351 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR a 351 " --> pdb=" O MET a 487 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA a 349 " --> pdb=" O LEU a 489 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N PHE a 468 " --> pdb=" O ARG a 350 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL a 352 " --> pdb=" O PHE a 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 455 through 458 removed outlier: 3.559A pdb=" N MET a 487 " --> pdb=" O THR a 351 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR a 351 " --> pdb=" O MET a 487 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA a 349 " --> pdb=" O LEU a 489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 365 through 367 removed outlier: 5.629A pdb=" N VAL a 366 " --> pdb=" O ILE a 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 376 through 379 removed outlier: 3.522A pdb=" N VAL a 432 " --> pdb=" O GLU a 378 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL a 405 " --> pdb=" O ILE a 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 512 through 513 removed outlier: 3.724A pdb=" N LYS a 518 " --> pdb=" O SER a 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 587 through 589 removed outlier: 3.548A pdb=" N LEU a 588 " --> pdb=" O ILE a 607 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 849 through 850 removed outlier: 6.967A pdb=" N THR a 856 " --> pdb=" O ILE a 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 1283 through 1292 removed outlier: 3.541A pdb=" N MET a1285 " --> pdb=" O VAL a1305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 1224 through 1228 removed outlier: 4.066A pdb=" N LEU a1236 " --> pdb=" O LEU a1197 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL a1242 " --> pdb=" O TRP a1191 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP a1191 " --> pdb=" O VAL a1242 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA a1149 " --> pdb=" O GLU a1196 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER a1150 " --> pdb=" O ARG i 45 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG i 45 " --> pdb=" O SER a1150 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE a1152 " --> pdb=" O VAL i 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 143 through 147 removed outlier: 5.608A pdb=" N VAL a1443 " --> pdb=" O ILE g 61 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY g 59 " --> pdb=" O ILE a1445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'f' and resid 143 through 147 removed outlier: 5.608A pdb=" N VAL a1443 " --> pdb=" O ILE g 61 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY g 59 " --> pdb=" O ILE a1445 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE g 79 " --> pdb=" O ILE g 45 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE g 45 " --> pdb=" O PHE g 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 69 through 73 removed outlier: 3.548A pdb=" N GLY b 93 " --> pdb=" O ASP b 131 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP b 131 " --> pdb=" O GLY b 93 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE b 95 " --> pdb=" O PHE b 129 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE b 129 " --> pdb=" O ILE b 95 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL b 97 " --> pdb=" O GLY b 127 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY b 127 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER b 126 " --> pdb=" O ARG b 169 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG b 169 " --> pdb=" O SER b 126 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU b 128 " --> pdb=" O ILE b 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 101 through 103 removed outlier: 3.986A pdb=" N VAL b 102 " --> pdb=" O HIS b 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 203 through 204 Processing sheet with id=AC2, first strand: chain 'b' and resid 404 through 407 Processing sheet with id=AC3, first strand: chain 'b' and resid 224 through 227 removed outlier: 4.277A pdb=" N HIS b 236 " --> pdb=" O LEU b 258 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU b 258 " --> pdb=" O HIS b 236 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 240 " --> pdb=" O LEU b 254 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN b 255 " --> pdb=" O THR b 272 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR b 268 " --> pdb=" O TYR b 259 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE b 269 " --> pdb=" O ILE b 280 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE b 280 " --> pdb=" O ILE b 269 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA b 271 " --> pdb=" O GLN b 278 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN b 278 " --> pdb=" O ALA b 271 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU b 273 " --> pdb=" O ILE b 276 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 544 through 545 Processing sheet with id=AC5, first strand: chain 'b' and resid 650 through 651 removed outlier: 3.546A pdb=" N GLU b 650 " --> pdb=" O GLU b 641 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 585 through 590 removed outlier: 3.683A pdb=" N HIS b 587 " --> pdb=" O VAL b 580 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL b 580 " --> pdb=" O HIS b 587 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL b 589 " --> pdb=" O THR b 578 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR b 578 " --> pdb=" O VAL b 589 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 792 through 796 removed outlier: 3.702A pdb=" N ILE b 795 " --> pdb=" O LEU b 854 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG b 857 " --> pdb=" O VAL b 968 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL b 966 " --> pdb=" O TYR b 859 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP b 861 " --> pdb=" O VAL b 964 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG b 967 " --> pdb=" O GLN b 951 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLN b 951 " --> pdb=" O ARG b 967 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG b 969 " --> pdb=" O VAL b 949 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL b 949 " --> pdb=" O ARG b 969 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 978 through 981 removed outlier: 5.451A pdb=" N LYS b 979 " --> pdb=" O LEU b1095 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU b1095 " --> pdb=" O LYS b 979 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA b 981 " --> pdb=" O GLN b1093 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE b1086 " --> pdb=" O ILE b 827 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE b 827 " --> pdb=" O PHE b1086 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU b1010 " --> pdb=" O ASN b 822 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE b 824 " --> pdb=" O LEU b1010 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE b1012 " --> pdb=" O ILE b 824 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA b 826 " --> pdb=" O ILE b1012 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N MET b 839 " --> pdb=" O GLY b 991 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR b 993 " --> pdb=" O MET b 839 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET b 841 " --> pdb=" O THR b 993 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 978 through 981 removed outlier: 5.451A pdb=" N LYS b 979 " --> pdb=" O LEU b1095 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU b1095 " --> pdb=" O LYS b 979 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA b 981 " --> pdb=" O GLN b1093 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 910 through 912 removed outlier: 6.819A pdb=" N THR b 939 " --> pdb=" O ILE b 911 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 1158 through 1162 Processing sheet with id=AD3, first strand: chain 'c' and resid 8 through 13 removed outlier: 6.609A pdb=" N ASP c 19 " --> pdb=" O ARG c 11 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA c 13 " --> pdb=" O ASN c 17 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN c 17 " --> pdb=" O ALA c 13 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE c 20 " --> pdb=" O MET c 230 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET c 230 " --> pdb=" O PHE c 20 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 119 through 120 removed outlier: 5.649A pdb=" N LYS c 160 " --> pdb=" O ILE c 46 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE c 46 " --> pdb=" O LYS c 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE l 67 " --> pdb=" O VAL c 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 72 through 74 removed outlier: 4.238A pdb=" N HIS c 131 " --> pdb=" O GLN c 73 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 111 through 112 Processing sheet with id=AD7, first strand: chain 'd' and resid 36 through 37 Processing sheet with id=AD8, first strand: chain 'e' and resid 60 through 62 removed outlier: 7.127A pdb=" N TRP e 79 " --> pdb=" O ILE e 109 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N VAL e 111 " --> pdb=" O TRP e 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 152 through 154 removed outlier: 3.761A pdb=" N LYS e 152 " --> pdb=" O ILE e 199 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE e 199 " --> pdb=" O LYS e 152 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 152 through 154 removed outlier: 3.761A pdb=" N LYS e 152 " --> pdb=" O ILE e 199 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE e 199 " --> pdb=" O LYS e 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 143 through 147 removed outlier: 3.682A pdb=" N VAL g 92 " --> pdb=" O GLU g 100 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU g 100 " --> pdb=" O VAL g 92 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS g 107 " --> pdb=" O ALA g 159 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'h' and resid 95 through 98 removed outlier: 4.290A pdb=" N TYR h 95 " --> pdb=" O ILE h 144 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE h 144 " --> pdb=" O TYR h 95 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU h 27 " --> pdb=" O SER h 13 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL h 15 " --> pdb=" O ARG h 25 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG h 25 " --> pdb=" O VAL h 15 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU h 122 " --> pdb=" O ASP h 41 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR h 116 " --> pdb=" O MET h 123 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU h 125 " --> pdb=" O VAL h 114 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL h 114 " --> pdb=" O LEU h 125 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU h 111 " --> pdb=" O GLU h 106 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU h 106 " --> pdb=" O LEU h 111 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA h 113 " --> pdb=" O PHE h 104 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE h 104 " --> pdb=" O ALA h 113 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR h 115 " --> pdb=" O TYR h 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'i' and resid 14 through 18 Processing sheet with id=AE5, first strand: chain 'i' and resid 84 through 87 Processing sheet with id=AE6, first strand: chain 'k' and resid 19 through 24 removed outlier: 4.534A pdb=" N ALA k 30 " --> pdb=" O ASP k 24 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE k 71 " --> pdb=" O PHE k 35 " (cutoff:3.500A) 1215 hydrogen bonds defined for protein. 3336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 8.99 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10155 1.33 - 1.45: 5894 1.45 - 1.57: 17652 1.57 - 1.70: 176 1.70 - 1.82: 290 Bond restraints: 34167 Sorted by residual: bond pdb=" C CYS b 523 " pdb=" N PRO b 524 " ideal model delta sigma weight residual 1.334 1.304 0.029 8.40e-03 1.42e+04 1.20e+01 bond pdb=" O3' A r 46 " pdb=" P U r 47 " ideal model delta sigma weight residual 1.607 1.556 0.051 1.50e-02 4.44e+03 1.17e+01 bond pdb=" O3' DA O -47 " pdb=" P DT O -46 " ideal model delta sigma weight residual 1.607 1.557 0.050 1.50e-02 4.44e+03 1.10e+01 bond pdb=" C MET a1433 " pdb=" N ALA a1434 " ideal model delta sigma weight residual 1.329 1.269 0.060 1.86e-02 2.89e+03 1.03e+01 bond pdb=" O3' U r 42 " pdb=" P A r 43 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.02e+01 ... (remaining 34162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 45952 2.98 - 5.96: 534 5.96 - 8.94: 49 8.94 - 11.92: 6 11.92 - 14.90: 4 Bond angle restraints: 46545 Sorted by residual: angle pdb=" O3' U r 40 " pdb=" C3' U r 40 " pdb=" C2' U r 40 " ideal model delta sigma weight residual 113.70 101.03 12.67 1.50e+00 4.44e-01 7.14e+01 angle pdb=" O2' U r 47 " pdb=" C2' U r 47 " pdb=" C1' U r 47 " ideal model delta sigma weight residual 108.40 96.09 12.31 1.50e+00 4.44e-01 6.73e+01 angle pdb=" O3' DG O -39 " pdb=" C3' DG O -39 " pdb=" C2' DG O -39 " ideal model delta sigma weight residual 111.50 99.45 12.05 1.50e+00 4.44e-01 6.46e+01 angle pdb=" N MET b1210 " pdb=" CA MET b1210 " pdb=" C MET b1210 " ideal model delta sigma weight residual 113.20 106.30 6.90 1.21e+00 6.83e-01 3.26e+01 angle pdb=" C ASN a 253 " pdb=" N GLU a 254 " pdb=" CA GLU a 254 " ideal model delta sigma weight residual 121.90 115.23 6.67 1.26e+00 6.30e-01 2.80e+01 ... (remaining 46540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 19936 35.09 - 70.18: 740 70.18 - 105.27: 48 105.27 - 140.36: 4 140.36 - 175.45: 2 Dihedral angle restraints: 20730 sinusoidal: 9238 harmonic: 11492 Sorted by residual: dihedral pdb=" CA ILE g 56 " pdb=" C ILE g 56 " pdb=" N GLN g 57 " pdb=" CA GLN g 57 " ideal model delta harmonic sigma weight residual 180.00 -144.21 -35.79 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA MET b 868 " pdb=" C MET b 868 " pdb=" N SER b 869 " pdb=" CA SER b 869 " ideal model delta harmonic sigma weight residual 180.00 -146.11 -33.89 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA ASP a 55 " pdb=" C ASP a 55 " pdb=" N PRO a 56 " pdb=" CA PRO a 56 " ideal model delta harmonic sigma weight residual 180.00 146.43 33.57 0 5.00e+00 4.00e-02 4.51e+01 ... (remaining 20727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 5049 0.106 - 0.212: 193 0.212 - 0.318: 2 0.318 - 0.424: 2 0.424 - 0.530: 1 Chirality restraints: 5247 Sorted by residual: chirality pdb=" C2' U r 40 " pdb=" C3' U r 40 " pdb=" O2' U r 40 " pdb=" C1' U r 40 " both_signs ideal model delta sigma weight residual False -2.75 -2.22 -0.53 2.00e-01 2.50e+01 7.03e+00 chirality pdb=" C3' DA O -42 " pdb=" C4' DA O -42 " pdb=" O3' DA O -42 " pdb=" C2' DA O -42 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C3' DG O -39 " pdb=" C4' DG O -39 " pdb=" O3' DG O -39 " pdb=" C2' DG O -39 " both_signs ideal model delta sigma weight residual False -2.66 -2.99 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 5244 not shown) Planarity restraints: 5704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U r 40 " 0.035 2.00e-02 2.50e+03 2.05e-02 9.49e+00 pdb=" N1 U r 40 " -0.049 2.00e-02 2.50e+03 pdb=" C2 U r 40 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U r 40 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U r 40 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U r 40 " 0.012 2.00e-02 2.50e+03 pdb=" O4 U r 40 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U r 40 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U r 40 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C r 39 " 0.043 2.00e-02 2.50e+03 1.99e-02 8.91e+00 pdb=" N1 C r 39 " -0.015 2.00e-02 2.50e+03 pdb=" C2 C r 39 " -0.007 2.00e-02 2.50e+03 pdb=" O2 C r 39 " -0.016 2.00e-02 2.50e+03 pdb=" N3 C r 39 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C r 39 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C r 39 " 0.024 2.00e-02 2.50e+03 pdb=" C5 C r 39 " -0.014 2.00e-02 2.50e+03 pdb=" C6 C r 39 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS k 102 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C LYS k 102 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS k 102 " -0.016 2.00e-02 2.50e+03 pdb=" N THR k 103 " -0.014 2.00e-02 2.50e+03 ... (remaining 5701 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 428 2.49 - 3.09: 26864 3.09 - 3.70: 55801 3.70 - 4.30: 74493 4.30 - 4.90: 114357 Nonbonded interactions: 271943 Sorted by model distance: nonbonded pdb=" O CYS a 67 " pdb="ZN ZN a1802 " model vdw 1.888 2.230 nonbonded pdb=" OD2 ASP a 481 " pdb="MG MG a1803 " model vdw 1.934 2.170 nonbonded pdb=" OP2 C r 48 " pdb="MG MG a1803 " model vdw 1.985 2.170 nonbonded pdb=" N THR a1394 " pdb="MG MG a1804 " model vdw 2.016 2.250 nonbonded pdb=" O ILE h 144 " pdb=" NH1 ARG h 145 " model vdw 2.056 3.120 ... (remaining 271938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.95 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 41.720 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 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 : 0.006 0.062 34197 Z= 0.293 Angle : 0.906 33.071 46581 Z= 0.505 Chirality : 0.048 0.530 5247 Planarity : 0.004 0.053 5704 Dihedral : 17.387 175.454 13290 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.40 % Favored : 87.58 % Rotamer: Outliers : 0.06 % Allowed : 0.55 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.11 % 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: -1.96 (0.13), residues: 3912 helix: 0.11 (0.15), residues: 1246 sheet: -1.39 (0.21), residues: 582 loop : -2.23 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG h 145 TYR 0.022 0.002 TYR b 833 PHE 0.028 0.002 PHE d 151 TRP 0.032 0.002 TRP b 466 HIS 0.009 0.001 HIS a 659 Details of bonding type rmsd covalent geometry : bond 0.00573 (34167) covalent geometry : angle 0.85711 (46545) hydrogen bonds : bond 0.19735 ( 1260) hydrogen bonds : angle 7.91120 ( 3470) metal coordination : bond 0.01389 ( 30) metal coordination : angle 10.61652 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 572 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 225 ASN cc_start: 0.8727 (t0) cc_final: 0.8307 (t0) REVERT: a 229 SER cc_start: 0.9345 (t) cc_final: 0.8894 (p) REVERT: a 234 MET cc_start: 0.9230 (tpt) cc_final: 0.8680 (tpt) REVERT: a 236 LEU cc_start: 0.9308 (mt) cc_final: 0.9011 (mt) REVERT: a 260 ASP cc_start: 0.8255 (m-30) cc_final: 0.7913 (m-30) REVERT: a 266 LEU cc_start: 0.9491 (mt) cc_final: 0.9219 (tt) REVERT: a 444 PHE cc_start: 0.8161 (t80) cc_final: 0.7674 (t80) REVERT: a 455 MET cc_start: 0.7837 (pmm) cc_final: 0.7406 (pmm) REVERT: a 456 MET cc_start: 0.8688 (mpp) cc_final: 0.7965 (mpp) REVERT: a 478 TYR cc_start: 0.8378 (m-80) cc_final: 0.7418 (m-80) REVERT: a 495 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8607 (mm-30) REVERT: a 515 GLN cc_start: 0.9338 (tm-30) cc_final: 0.8781 (tm-30) REVERT: a 605 MET cc_start: 0.6457 (tpp) cc_final: 0.6124 (tpp) REVERT: a 662 PHE cc_start: 0.7415 (t80) cc_final: 0.6880 (t80) REVERT: a 826 ASP cc_start: 0.8908 (t70) cc_final: 0.8669 (t70) REVERT: a 852 TYR cc_start: 0.7266 (m-10) cc_final: 0.7046 (m-10) REVERT: a 994 GLN cc_start: 0.8089 (pt0) cc_final: 0.7630 (tt0) REVERT: a 1037 LEU cc_start: 0.5070 (mm) cc_final: 0.3961 (tp) REVERT: a 1074 GLU cc_start: 0.8230 (tt0) cc_final: 0.7471 (tt0) REVERT: a 1317 MET cc_start: 0.8714 (tmm) cc_final: 0.8423 (tmm) REVERT: a 1430 LEU cc_start: 0.8746 (tp) cc_final: 0.8051 (tp) REVERT: a 1454 MET cc_start: 0.6344 (mpp) cc_final: 0.5766 (mpp) REVERT: b 181 LEU cc_start: 0.9208 (mt) cc_final: 0.8952 (tp) REVERT: b 310 MET cc_start: 0.9191 (pmm) cc_final: 0.8923 (pmm) REVERT: b 391 ASP cc_start: 0.9470 (m-30) cc_final: 0.8977 (t0) REVERT: b 412 LEU cc_start: 0.9119 (mt) cc_final: 0.8837 (mt) REVERT: b 514 LEU cc_start: 0.9248 (tp) cc_final: 0.8845 (tp) REVERT: b 541 LEU cc_start: 0.9397 (pp) cc_final: 0.8896 (mp) REVERT: b 597 MET cc_start: 0.9137 (tpp) cc_final: 0.8872 (tpt) REVERT: b 615 MET cc_start: 0.9029 (pmm) cc_final: 0.8646 (pmm) REVERT: b 834 ASN cc_start: 0.8756 (p0) cc_final: 0.8482 (p0) REVERT: b 837 ASP cc_start: 0.9223 (m-30) cc_final: 0.8936 (m-30) REVERT: b 987 LYS cc_start: 0.8488 (pttt) cc_final: 0.8209 (ptmt) REVERT: b 1013 ASN cc_start: 0.9103 (t0) cc_final: 0.8903 (t0) REVERT: b 1128 LEU cc_start: 0.8933 (mp) cc_final: 0.8647 (mp) REVERT: b 1133 MET cc_start: 0.8776 (mtp) cc_final: 0.8555 (mmm) REVERT: b 1208 MET cc_start: 0.8591 (pmm) cc_final: 0.7676 (pmm) REVERT: c 61 GLU cc_start: 0.9304 (pt0) cc_final: 0.8993 (pm20) REVERT: d 33 PHE cc_start: 0.8631 (m-80) cc_final: 0.8320 (m-10) REVERT: d 70 PHE cc_start: 0.7413 (m-10) cc_final: 0.7115 (m-80) REVERT: e 22 MET cc_start: 0.9485 (tmm) cc_final: 0.9259 (tmm) REVERT: e 60 PHE cc_start: 0.7570 (t80) cc_final: 0.7336 (t80) REVERT: e 114 ASN cc_start: 0.8911 (m-40) cc_final: 0.8263 (m110) REVERT: f 133 VAL cc_start: 0.8151 (m) cc_final: 0.7909 (m) REVERT: g 3 PHE cc_start: 0.8024 (m-10) cc_final: 0.7161 (m-80) REVERT: g 42 PHE cc_start: 0.6474 (m-80) cc_final: 0.6244 (m-80) REVERT: h 123 MET cc_start: 0.6795 (ppp) cc_final: 0.6547 (ppp) REVERT: i 87 GLN cc_start: 0.6183 (pp30) cc_final: 0.5728 (pp30) REVERT: j 1 MET cc_start: 0.7381 (mmm) cc_final: 0.7114 (mmm) REVERT: j 16 ASP cc_start: 0.8724 (p0) cc_final: 0.7632 (t0) REVERT: l 38 LEU cc_start: 0.8174 (mm) cc_final: 0.7849 (mm) outliers start: 2 outliers final: 0 residues processed: 574 average time/residue: 0.2190 time to fit residues: 205.2556 Evaluate side-chains 378 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 GLN a 394 ASN a 447 GLN ** a 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 611 GLN a 742 ASN ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 786 HIS ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1009 ASN ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN b 357 GLN ** b 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 ASN e 54 GLN e 146 HIS g 158 HIS ** h 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 22 ASN ** i 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.073781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.048977 restraints weight = 129134.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.051022 restraints weight = 59909.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.052394 restraints weight = 37101.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.053313 restraints weight = 26916.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.053914 restraints weight = 21794.468| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 34197 Z= 0.205 Angle : 0.822 26.728 46581 Z= 0.412 Chirality : 0.047 0.211 5247 Planarity : 0.005 0.066 5704 Dihedral : 16.941 175.808 5419 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 1.15 % Allowed : 11.94 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.05 % 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: -1.70 (0.13), residues: 3912 helix: 0.33 (0.14), residues: 1289 sheet: -1.15 (0.21), residues: 579 loop : -2.15 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a1100 TYR 0.023 0.002 TYR e 208 PHE 0.030 0.002 PHE d 151 TRP 0.024 0.002 TRP a 656 HIS 0.007 0.001 HIS b 515 Details of bonding type rmsd covalent geometry : bond 0.00447 (34167) covalent geometry : angle 0.77327 (46545) hydrogen bonds : bond 0.05133 ( 1260) hydrogen bonds : angle 6.10973 ( 3470) metal coordination : bond 0.01190 ( 30) metal coordination : angle 10.10958 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 414 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8054 (tpt) cc_final: 0.7833 (tpt) REVERT: a 72 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8135 (mp0) REVERT: a 74 MET cc_start: 0.8696 (ttm) cc_final: 0.8465 (ttt) REVERT: a 108 MET cc_start: 0.8317 (pmm) cc_final: 0.7869 (pmm) REVERT: a 225 ASN cc_start: 0.8987 (t0) cc_final: 0.8576 (t0) REVERT: a 229 SER cc_start: 0.9382 (t) cc_final: 0.8913 (p) REVERT: a 236 LEU cc_start: 0.9222 (mt) cc_final: 0.8943 (mt) REVERT: a 260 ASP cc_start: 0.8183 (m-30) cc_final: 0.7818 (m-30) REVERT: a 266 LEU cc_start: 0.9557 (mt) cc_final: 0.9301 (tt) REVERT: a 313 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8603 (tp40) REVERT: a 339 ASN cc_start: 0.9058 (t0) cc_final: 0.8771 (t0) REVERT: a 374 LEU cc_start: 0.8039 (mp) cc_final: 0.7768 (pt) REVERT: a 444 PHE cc_start: 0.8222 (t80) cc_final: 0.7623 (t80) REVERT: a 455 MET cc_start: 0.7456 (pmm) cc_final: 0.6903 (pmm) REVERT: a 456 MET cc_start: 0.8514 (mpp) cc_final: 0.7647 (mpp) REVERT: a 515 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8431 (tm-30) REVERT: a 521 MET cc_start: 0.9028 (tpp) cc_final: 0.7975 (mmm) REVERT: a 712 GLU cc_start: 0.9523 (mp0) cc_final: 0.9312 (mp0) REVERT: a 748 MET cc_start: 0.8744 (mtt) cc_final: 0.8381 (mtt) REVERT: a 818 MET cc_start: 0.9565 (mmt) cc_final: 0.9355 (mmt) REVERT: a 826 ASP cc_start: 0.8723 (t70) cc_final: 0.8517 (t70) REVERT: a 849 MET cc_start: 0.7860 (ppp) cc_final: 0.6795 (tmm) REVERT: a 1317 MET cc_start: 0.9032 (tmm) cc_final: 0.8488 (tmm) REVERT: a 1421 CYS cc_start: 0.8275 (t) cc_final: 0.7904 (m) REVERT: a 1444 MET cc_start: 0.8806 (tpt) cc_final: 0.8593 (mmm) REVERT: b 181 LEU cc_start: 0.9112 (mt) cc_final: 0.8731 (tt) REVERT: b 361 LEU cc_start: 0.9281 (tp) cc_final: 0.9076 (tp) REVERT: b 412 LEU cc_start: 0.9150 (mt) cc_final: 0.8789 (mt) REVERT: b 481 GLN cc_start: 0.9036 (mt0) cc_final: 0.8302 (mt0) REVERT: b 542 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.9014 (mtt) REVERT: b 597 MET cc_start: 0.9545 (tpp) cc_final: 0.8884 (tpt) REVERT: b 698 GLU cc_start: 0.9477 (mt-10) cc_final: 0.8873 (mt-10) REVERT: b 796 LEU cc_start: 0.8896 (mt) cc_final: 0.8655 (mt) REVERT: b 809 MET cc_start: 0.8474 (mpp) cc_final: 0.8113 (pmm) REVERT: b 837 ASP cc_start: 0.9150 (m-30) cc_final: 0.8925 (m-30) REVERT: b 1072 MET cc_start: 0.8215 (tpt) cc_final: 0.7704 (tpt) REVERT: b 1128 LEU cc_start: 0.8941 (mp) cc_final: 0.8651 (mp) REVERT: b 1193 GLN cc_start: 0.8856 (pt0) cc_final: 0.8436 (pt0) REVERT: b 1208 MET cc_start: 0.8432 (pmm) cc_final: 0.7508 (pmm) REVERT: b 1210 MET cc_start: 0.8733 (mmm) cc_final: 0.8198 (mmm) REVERT: c 61 GLU cc_start: 0.9291 (pt0) cc_final: 0.8777 (pm20) REVERT: c 125 MET cc_start: 0.7601 (mpp) cc_final: 0.7379 (mpp) REVERT: c 169 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8888 (ptpt) REVERT: e 60 PHE cc_start: 0.8505 (t80) cc_final: 0.8222 (t80) REVERT: e 75 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7896 (ppp) REVERT: e 93 MET cc_start: 0.9560 (ppp) cc_final: 0.9233 (ppp) REVERT: e 114 ASN cc_start: 0.8787 (m-40) cc_final: 0.8203 (m110) REVERT: f 89 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8232 (mt-10) REVERT: h 118 PHE cc_start: 0.8669 (m-80) cc_final: 0.8469 (m-10) REVERT: h 123 MET cc_start: 0.8503 (ppp) cc_final: 0.7920 (ppp) REVERT: i 87 GLN cc_start: 0.8017 (pp30) cc_final: 0.7721 (pp30) REVERT: k 10 PHE cc_start: 0.7774 (t80) cc_final: 0.7550 (t80) REVERT: k 39 ASP cc_start: 0.9088 (t0) cc_final: 0.8504 (t0) REVERT: k 108 GLU cc_start: 0.9385 (tp30) cc_final: 0.9027 (tt0) outliers start: 40 outliers final: 20 residues processed: 438 average time/residue: 0.2084 time to fit residues: 153.3778 Evaluate side-chains 378 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 355 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 86 LEU Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 394 ASN Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 1306 LEU Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 179 CYS Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 539 LEU Chi-restraints excluded: chain b residue 542 MET Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 882 THR Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 169 LYS Chi-restraints excluded: chain e residue 75 MET Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 90 THR Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain j residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 352 optimal weight: 50.0000 chunk 91 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 309 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 176 optimal weight: 0.0870 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 395 GLN ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 821 GLN b 822 ASN ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 158 HIS h 35 GLN h 128 ASN h 131 ASN ** i 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.075347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050224 restraints weight = 128085.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.052327 restraints weight = 58934.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.053741 restraints weight = 36274.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.054678 restraints weight = 26285.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.055315 restraints weight = 21243.236| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 34197 Z= 0.146 Angle : 0.744 19.253 46581 Z= 0.371 Chirality : 0.045 0.217 5247 Planarity : 0.004 0.053 5704 Dihedral : 16.817 178.145 5419 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 1.76 % Allowed : 16.26 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.44 (0.14), residues: 3912 helix: 0.58 (0.15), residues: 1283 sheet: -1.07 (0.22), residues: 556 loop : -2.00 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG c 84 TYR 0.017 0.001 TYR a 551 PHE 0.025 0.002 PHE d 151 TRP 0.014 0.001 TRP a 185 HIS 0.009 0.001 HIS b1015 Details of bonding type rmsd covalent geometry : bond 0.00321 (34167) covalent geometry : angle 0.71007 (46545) hydrogen bonds : bond 0.04293 ( 1260) hydrogen bonds : angle 5.50890 ( 3470) metal coordination : bond 0.00908 ( 30) metal coordination : angle 7.99485 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 423 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 72 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8268 (mp0) REVERT: a 92 HIS cc_start: 0.7724 (t-90) cc_final: 0.7016 (t-90) REVERT: a 108 MET cc_start: 0.8439 (pmm) cc_final: 0.7918 (pmm) REVERT: a 234 MET cc_start: 0.9443 (tpt) cc_final: 0.9050 (tpp) REVERT: a 236 LEU cc_start: 0.9206 (mt) cc_final: 0.8926 (mt) REVERT: a 260 ASP cc_start: 0.8160 (m-30) cc_final: 0.7845 (m-30) REVERT: a 313 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8559 (tp40) REVERT: a 339 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8751 (t0) REVERT: a 341 MET cc_start: 0.8859 (tpp) cc_final: 0.8535 (tpp) REVERT: a 444 PHE cc_start: 0.8314 (t80) cc_final: 0.7547 (t80) REVERT: a 453 MET cc_start: 0.9294 (mpp) cc_final: 0.9041 (mpp) REVERT: a 455 MET cc_start: 0.7393 (pmm) cc_final: 0.6678 (pmm) REVERT: a 456 MET cc_start: 0.8366 (mpp) cc_final: 0.7629 (mpp) REVERT: a 515 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8451 (tm-30) REVERT: a 521 MET cc_start: 0.8922 (tpp) cc_final: 0.8080 (mmm) REVERT: a 550 LEU cc_start: 0.9331 (mm) cc_final: 0.9069 (tp) REVERT: a 605 MET cc_start: 0.8214 (tpp) cc_final: 0.7344 (mmt) REVERT: a 737 LEU cc_start: 0.9043 (tp) cc_final: 0.8819 (tp) REVERT: a 748 MET cc_start: 0.8469 (mtt) cc_final: 0.8068 (mtt) REVERT: a 1317 MET cc_start: 0.9002 (tmm) cc_final: 0.8582 (tmm) REVERT: a 1375 MET cc_start: 0.9060 (tmm) cc_final: 0.8700 (tmm) REVERT: a 1403 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6622 (mm-30) REVERT: a 1421 CYS cc_start: 0.8365 (t) cc_final: 0.8041 (m) REVERT: a 1426 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8964 (mm-30) REVERT: b 181 LEU cc_start: 0.9098 (mt) cc_final: 0.8526 (tt) REVERT: b 361 LEU cc_start: 0.9215 (tp) cc_final: 0.8961 (tp) REVERT: b 412 LEU cc_start: 0.9181 (mt) cc_final: 0.8848 (mt) REVERT: b 481 GLN cc_start: 0.9035 (mt0) cc_final: 0.8253 (mt0) REVERT: b 542 MET cc_start: 0.9347 (mtp) cc_final: 0.7951 (mtt) REVERT: b 597 MET cc_start: 0.9558 (tpp) cc_final: 0.8934 (tpt) REVERT: b 684 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9049 (tt) REVERT: b 697 GLU cc_start: 0.9001 (tp30) cc_final: 0.8213 (tp30) REVERT: b 698 GLU cc_start: 0.9494 (mt-10) cc_final: 0.8807 (mt-10) REVERT: b 747 MET cc_start: 0.9073 (mmp) cc_final: 0.8074 (mmp) REVERT: b 834 ASN cc_start: 0.8482 (p0) cc_final: 0.8025 (p0) REVERT: b 1013 ASN cc_start: 0.8820 (t0) cc_final: 0.8509 (t0) REVERT: b 1021 MET cc_start: 0.7882 (mmt) cc_final: 0.7640 (mmt) REVERT: b 1098 MET cc_start: 0.8237 (mmt) cc_final: 0.7856 (mmp) REVERT: b 1128 LEU cc_start: 0.8866 (mp) cc_final: 0.8586 (mp) REVERT: b 1193 GLN cc_start: 0.8854 (pt0) cc_final: 0.8452 (pt0) REVERT: b 1208 MET cc_start: 0.8482 (pmm) cc_final: 0.7545 (pmm) REVERT: b 1210 MET cc_start: 0.8777 (mmm) cc_final: 0.8186 (mmm) REVERT: c 58 LEU cc_start: 0.9028 (mt) cc_final: 0.8254 (tp) REVERT: e 22 MET cc_start: 0.9505 (tmm) cc_final: 0.9286 (tmm) REVERT: e 60 PHE cc_start: 0.8432 (t80) cc_final: 0.8202 (t80) REVERT: e 75 MET cc_start: 0.8286 (tmm) cc_final: 0.8009 (ppp) REVERT: e 93 MET cc_start: 0.9530 (ppp) cc_final: 0.9132 (ppp) REVERT: e 114 ASN cc_start: 0.8863 (m-40) cc_final: 0.8307 (m110) REVERT: f 89 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8307 (mt-10) REVERT: f 103 MET cc_start: 0.9223 (tmm) cc_final: 0.8785 (tmm) REVERT: f 104 ASN cc_start: 0.9509 (t0) cc_final: 0.9252 (t0) REVERT: g 25 TYR cc_start: 0.9069 (t80) cc_final: 0.8838 (t80) REVERT: g 106 MET cc_start: 0.3742 (pmm) cc_final: 0.3416 (pmm) REVERT: h 97 MET cc_start: 0.8770 (tmm) cc_final: 0.8441 (tmm) REVERT: h 118 PHE cc_start: 0.8791 (m-80) cc_final: 0.8493 (m-10) REVERT: h 123 MET cc_start: 0.8646 (ppp) cc_final: 0.7983 (ppp) REVERT: i 87 GLN cc_start: 0.7966 (pp30) cc_final: 0.7636 (pp30) REVERT: k 1 MET cc_start: 0.9432 (tpp) cc_final: 0.9220 (tpp) REVERT: k 39 ASP cc_start: 0.8737 (t0) cc_final: 0.8484 (t0) REVERT: k 108 GLU cc_start: 0.9406 (tp30) cc_final: 0.9038 (tt0) outliers start: 61 outliers final: 26 residues processed: 459 average time/residue: 0.2111 time to fit residues: 162.6488 Evaluate side-chains 391 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 363 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 339 ASN Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 539 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain e residue 150 VAL Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain j residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 275 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 311 optimal weight: 0.8980 chunk 298 optimal weight: 20.0000 chunk 307 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 124 GLN ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 650 GLN a 659 HIS ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 821 GLN ** b 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 147 HIS ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 158 HIS ** h 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.075790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.050623 restraints weight = 127387.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.052703 restraints weight = 59842.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054111 restraints weight = 37186.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.055062 restraints weight = 27037.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.055676 restraints weight = 21869.693| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34197 Z= 0.134 Angle : 0.735 21.439 46581 Z= 0.363 Chirality : 0.044 0.359 5247 Planarity : 0.004 0.053 5704 Dihedral : 16.743 178.024 5419 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 1.96 % Allowed : 18.14 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.37 (0.14), residues: 3912 helix: 0.62 (0.15), residues: 1292 sheet: -1.03 (0.22), residues: 566 loop : -1.95 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 807 TYR 0.014 0.001 TYR a 551 PHE 0.025 0.001 PHE d 151 TRP 0.013 0.001 TRP a 185 HIS 0.017 0.001 HIS b1015 Details of bonding type rmsd covalent geometry : bond 0.00295 (34167) covalent geometry : angle 0.70245 (46545) hydrogen bonds : bond 0.03874 ( 1260) hydrogen bonds : angle 5.20625 ( 3470) metal coordination : bond 0.00944 ( 30) metal coordination : angle 7.81784 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 419 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8046 (tpt) cc_final: 0.7820 (tpt) REVERT: a 72 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8186 (mp0) REVERT: a 92 HIS cc_start: 0.7482 (t-90) cc_final: 0.7102 (t-170) REVERT: a 108 MET cc_start: 0.8514 (pmm) cc_final: 0.8065 (pmm) REVERT: a 234 MET cc_start: 0.9464 (tpt) cc_final: 0.8644 (ttt) REVERT: a 236 LEU cc_start: 0.9137 (mt) cc_final: 0.8825 (mt) REVERT: a 260 ASP cc_start: 0.8190 (m-30) cc_final: 0.7903 (m-30) REVERT: a 304 MET cc_start: 0.9472 (tpt) cc_final: 0.9258 (tpt) REVERT: a 313 GLN cc_start: 0.8744 (tp-100) cc_final: 0.8518 (tp40) REVERT: a 339 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8748 (t0) REVERT: a 341 MET cc_start: 0.8926 (tpp) cc_final: 0.8360 (tpp) REVERT: a 444 PHE cc_start: 0.8195 (t80) cc_final: 0.7590 (t80) REVERT: a 453 MET cc_start: 0.9282 (mpp) cc_final: 0.8769 (mmm) REVERT: a 455 MET cc_start: 0.7375 (pmm) cc_final: 0.6977 (pmm) REVERT: a 456 MET cc_start: 0.8389 (mpp) cc_final: 0.7825 (mpp) REVERT: a 515 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8297 (tm-30) REVERT: a 521 MET cc_start: 0.8825 (tpp) cc_final: 0.7988 (mmm) REVERT: a 550 LEU cc_start: 0.9322 (mm) cc_final: 0.9014 (tp) REVERT: a 605 MET cc_start: 0.8296 (tpp) cc_final: 0.7268 (mmt) REVERT: a 612 ILE cc_start: 0.9048 (mt) cc_final: 0.8625 (tp) REVERT: a 737 LEU cc_start: 0.9010 (tp) cc_final: 0.8727 (tp) REVERT: a 849 MET cc_start: 0.7692 (ppp) cc_final: 0.7075 (tmm) REVERT: a 1013 ASP cc_start: 0.8685 (m-30) cc_final: 0.8367 (m-30) REVERT: a 1062 GLU cc_start: 0.9340 (tt0) cc_final: 0.8890 (tt0) REVERT: a 1074 GLU cc_start: 0.7618 (tt0) cc_final: 0.6865 (tt0) REVERT: a 1317 MET cc_start: 0.8972 (tmm) cc_final: 0.8738 (tmm) REVERT: a 1364 ASN cc_start: 0.8622 (t0) cc_final: 0.8256 (t0) REVERT: a 1375 MET cc_start: 0.9052 (tmm) cc_final: 0.8674 (tmm) REVERT: a 1403 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6542 (mm-30) REVERT: a 1421 CYS cc_start: 0.8310 (t) cc_final: 0.7983 (m) REVERT: a 1426 GLU cc_start: 0.9251 (mm-30) cc_final: 0.9026 (mm-30) REVERT: b 181 LEU cc_start: 0.9073 (mt) cc_final: 0.8511 (tt) REVERT: b 361 LEU cc_start: 0.9167 (tp) cc_final: 0.8896 (tp) REVERT: b 412 LEU cc_start: 0.9135 (mt) cc_final: 0.8825 (mt) REVERT: b 481 GLN cc_start: 0.8999 (mt0) cc_final: 0.8257 (mt0) REVERT: b 521 LEU cc_start: 0.9462 (tp) cc_final: 0.9169 (mm) REVERT: b 529 GLU cc_start: 0.8198 (pm20) cc_final: 0.7956 (pm20) REVERT: b 542 MET cc_start: 0.9320 (mtp) cc_final: 0.8772 (mtt) REVERT: b 597 MET cc_start: 0.9576 (tpp) cc_final: 0.9065 (tpt) REVERT: b 616 ILE cc_start: 0.8621 (pt) cc_final: 0.8314 (mp) REVERT: b 684 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9075 (tt) REVERT: b 698 GLU cc_start: 0.9449 (mt-10) cc_final: 0.8956 (mt-10) REVERT: b 705 MET cc_start: 0.8563 (tmm) cc_final: 0.8256 (tmm) REVERT: b 834 ASN cc_start: 0.8418 (p0) cc_final: 0.7846 (p0) REVERT: b 987 LYS cc_start: 0.8370 (ptmt) cc_final: 0.7840 (ptmt) REVERT: b 1021 MET cc_start: 0.7811 (mmt) cc_final: 0.7507 (mmt) REVERT: b 1193 GLN cc_start: 0.8780 (pt0) cc_final: 0.8325 (pt0) REVERT: b 1208 MET cc_start: 0.8511 (pmm) cc_final: 0.7641 (pmm) REVERT: c 58 LEU cc_start: 0.8957 (mt) cc_final: 0.8198 (tp) REVERT: e 21 GLU cc_start: 0.9626 (OUTLIER) cc_final: 0.9198 (tt0) REVERT: e 22 MET cc_start: 0.9516 (tmm) cc_final: 0.9288 (tmm) REVERT: e 75 MET cc_start: 0.8315 (tmm) cc_final: 0.8092 (ppp) REVERT: e 93 MET cc_start: 0.9528 (ppp) cc_final: 0.9113 (ppp) REVERT: e 114 ASN cc_start: 0.8915 (m-40) cc_final: 0.8384 (m110) REVERT: f 89 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8210 (mt-10) REVERT: f 103 MET cc_start: 0.9217 (tmm) cc_final: 0.8422 (tmm) REVERT: f 104 ASN cc_start: 0.9502 (t0) cc_final: 0.9231 (t0) REVERT: g 25 TYR cc_start: 0.9076 (t80) cc_final: 0.8833 (t80) REVERT: h 63 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8455 (mt) REVERT: h 89 LEU cc_start: 0.9307 (tt) cc_final: 0.8824 (pt) REVERT: h 97 MET cc_start: 0.8608 (tmm) cc_final: 0.8363 (tmm) REVERT: h 118 PHE cc_start: 0.8903 (m-80) cc_final: 0.8574 (m-10) REVERT: h 123 MET cc_start: 0.8723 (ppp) cc_final: 0.8038 (ppp) REVERT: i 48 LEU cc_start: 0.9389 (tt) cc_final: 0.9096 (pp) REVERT: j 28 ASP cc_start: 0.8844 (m-30) cc_final: 0.8560 (m-30) REVERT: j 58 GLU cc_start: 0.9573 (mm-30) cc_final: 0.8808 (mp0) REVERT: k 10 PHE cc_start: 0.7477 (t80) cc_final: 0.7018 (t80) REVERT: k 108 GLU cc_start: 0.9404 (tp30) cc_final: 0.9007 (tt0) outliers start: 68 outliers final: 35 residues processed: 464 average time/residue: 0.2043 time to fit residues: 161.0586 Evaluate side-chains 411 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 372 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 124 GLN Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 339 ASN Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 645 LEU Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 965 GLN Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 603 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 150 VAL Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain k residue 41 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 17 optimal weight: 40.0000 chunk 30 optimal weight: 5.9990 chunk 136 optimal weight: 0.3980 chunk 93 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 357 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1195 HIS ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN h 131 ASN ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.074927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049909 restraints weight = 128946.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.051959 restraints weight = 59987.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.053361 restraints weight = 37230.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.054258 restraints weight = 27003.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.054923 restraints weight = 21931.336| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34197 Z= 0.174 Angle : 0.735 19.036 46581 Z= 0.368 Chirality : 0.044 0.312 5247 Planarity : 0.004 0.054 5704 Dihedral : 16.755 177.803 5419 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 2.48 % Allowed : 19.00 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.03 % 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: -1.32 (0.14), residues: 3912 helix: 0.69 (0.15), residues: 1299 sheet: -0.96 (0.22), residues: 555 loop : -1.95 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a1100 TYR 0.019 0.001 TYR b 833 PHE 0.027 0.002 PHE b 203 TRP 0.013 0.001 TRP a 185 HIS 0.012 0.001 HIS b1015 Details of bonding type rmsd covalent geometry : bond 0.00387 (34167) covalent geometry : angle 0.70540 (46545) hydrogen bonds : bond 0.03881 ( 1260) hydrogen bonds : angle 5.11683 ( 3470) metal coordination : bond 0.01018 ( 30) metal coordination : angle 7.49741 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 371 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 72 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8287 (mp0) REVERT: a 95 PHE cc_start: 0.8317 (m-10) cc_final: 0.7848 (m-10) REVERT: a 108 MET cc_start: 0.8666 (pmm) cc_final: 0.8193 (pmm) REVERT: a 122 MET cc_start: 0.9056 (pmm) cc_final: 0.8789 (pmm) REVERT: a 234 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.8593 (ttt) REVERT: a 260 ASP cc_start: 0.8210 (m-30) cc_final: 0.7890 (m-30) REVERT: a 313 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8606 (tp40) REVERT: a 339 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8819 (t0) REVERT: a 341 MET cc_start: 0.8896 (tpp) cc_final: 0.8249 (tpp) REVERT: a 444 PHE cc_start: 0.8373 (t80) cc_final: 0.7668 (t80) REVERT: a 453 MET cc_start: 0.9292 (mpp) cc_final: 0.8926 (mmm) REVERT: a 455 MET cc_start: 0.7272 (pmm) cc_final: 0.6451 (pmm) REVERT: a 456 MET cc_start: 0.8485 (mpp) cc_final: 0.7293 (mpp) REVERT: a 515 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8348 (tm-30) REVERT: a 550 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9095 (tp) REVERT: a 605 MET cc_start: 0.8381 (tpp) cc_final: 0.7299 (mmt) REVERT: a 612 ILE cc_start: 0.9125 (mt) cc_final: 0.8755 (tp) REVERT: a 708 MET cc_start: 0.8029 (mtm) cc_final: 0.7527 (pmm) REVERT: a 737 LEU cc_start: 0.9069 (tp) cc_final: 0.8750 (tp) REVERT: a 748 MET cc_start: 0.8830 (mtt) cc_final: 0.8367 (mtt) REVERT: a 1013 ASP cc_start: 0.8776 (m-30) cc_final: 0.8467 (m-30) REVERT: a 1062 GLU cc_start: 0.9401 (tt0) cc_final: 0.9177 (tt0) REVERT: a 1074 GLU cc_start: 0.7798 (tt0) cc_final: 0.6951 (tt0) REVERT: a 1317 MET cc_start: 0.9010 (tmm) cc_final: 0.8761 (tmm) REVERT: a 1375 MET cc_start: 0.9051 (tmm) cc_final: 0.8637 (tmm) REVERT: a 1377 THR cc_start: 0.8656 (t) cc_final: 0.8450 (t) REVERT: a 1403 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6689 (mm-30) REVERT: b 181 LEU cc_start: 0.9089 (mt) cc_final: 0.8497 (tt) REVERT: b 361 LEU cc_start: 0.9171 (tp) cc_final: 0.8893 (tp) REVERT: b 412 LEU cc_start: 0.9108 (mt) cc_final: 0.8779 (mt) REVERT: b 473 MET cc_start: 0.6827 (ptt) cc_final: 0.6623 (ptp) REVERT: b 542 MET cc_start: 0.9278 (mtp) cc_final: 0.8698 (mtt) REVERT: b 597 MET cc_start: 0.9587 (tpp) cc_final: 0.9041 (tpt) REVERT: b 684 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9053 (tt) REVERT: b 698 GLU cc_start: 0.9540 (mt-10) cc_final: 0.8979 (mt-10) REVERT: b 705 MET cc_start: 0.8609 (tmm) cc_final: 0.8402 (tmm) REVERT: b 834 ASN cc_start: 0.8389 (p0) cc_final: 0.7942 (p0) REVERT: b 987 LYS cc_start: 0.8437 (ptmt) cc_final: 0.7874 (ptmt) REVERT: b 1013 ASN cc_start: 0.8676 (t0) cc_final: 0.8407 (t0) REVERT: b 1021 MET cc_start: 0.7869 (mmt) cc_final: 0.7481 (mmp) REVERT: b 1111 MET cc_start: 0.8816 (mmp) cc_final: 0.8591 (tpp) REVERT: b 1193 GLN cc_start: 0.8862 (pt0) cc_final: 0.8438 (pt0) REVERT: b 1201 LYS cc_start: 0.9310 (pptt) cc_final: 0.8998 (ttpp) REVERT: b 1208 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7716 (pmm) REVERT: c 58 LEU cc_start: 0.8972 (mt) cc_final: 0.8234 (tp) REVERT: c 60 ASP cc_start: 0.8400 (t70) cc_final: 0.8135 (t70) REVERT: e 5 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8702 (t0) REVERT: e 60 PHE cc_start: 0.8391 (t80) cc_final: 0.8151 (t80) REVERT: e 114 ASN cc_start: 0.8956 (m-40) cc_final: 0.8417 (m110) REVERT: f 89 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8232 (mt-10) REVERT: f 103 MET cc_start: 0.9226 (tmm) cc_final: 0.8511 (tmm) REVERT: f 104 ASN cc_start: 0.9503 (t0) cc_final: 0.9240 (t0) REVERT: g 22 MET cc_start: 0.9314 (ppp) cc_final: 0.9079 (ppp) REVERT: g 25 TYR cc_start: 0.9106 (t80) cc_final: 0.8891 (t80) REVERT: g 69 GLU cc_start: 0.8907 (tt0) cc_final: 0.8294 (tp30) REVERT: h 97 MET cc_start: 0.8798 (tmm) cc_final: 0.8432 (tmm) REVERT: h 116 TYR cc_start: 0.8542 (m-80) cc_final: 0.8150 (m-80) REVERT: h 118 PHE cc_start: 0.8972 (m-80) cc_final: 0.8560 (m-10) REVERT: h 123 MET cc_start: 0.8837 (ppp) cc_final: 0.8177 (ppp) REVERT: i 48 LEU cc_start: 0.9468 (tt) cc_final: 0.9200 (pp) REVERT: j 58 GLU cc_start: 0.9583 (mm-30) cc_final: 0.8799 (mp0) REVERT: k 39 ASP cc_start: 0.8678 (t0) cc_final: 0.8463 (t0) REVERT: k 106 GLU cc_start: 0.9809 (tt0) cc_final: 0.9220 (tm-30) REVERT: k 108 GLU cc_start: 0.9372 (tp30) cc_final: 0.9011 (tt0) outliers start: 86 outliers final: 53 residues processed: 434 average time/residue: 0.1854 time to fit residues: 138.4544 Evaluate side-chains 415 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 356 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 339 ASN Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 511 ILE Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 565 ILE Chi-restraints excluded: chain a residue 645 LEU Chi-restraints excluded: chain a residue 690 VAL Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 856 THR Chi-restraints excluded: chain a residue 965 GLN Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 174 LEU Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 466 TRP Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 238 ILE Chi-restraints excluded: chain e residue 5 ASN Chi-restraints excluded: chain e residue 150 VAL Chi-restraints excluded: chain e residue 178 ILE Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 163 ILE Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain i residue 108 HIS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain k residue 63 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 358 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 177 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 365 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 342 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 124 GLN ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 253 ASN ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 447 GLN ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1432 GLN ** b 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 203 GLN ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.074320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049402 restraints weight = 130033.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.051433 restraints weight = 60753.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.052811 restraints weight = 37746.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053733 restraints weight = 27432.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.054351 restraints weight = 22217.377| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34197 Z= 0.190 Angle : 0.746 17.970 46581 Z= 0.374 Chirality : 0.044 0.290 5247 Planarity : 0.004 0.054 5704 Dihedral : 16.785 177.838 5419 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 2.85 % Allowed : 19.58 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % 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: -1.33 (0.14), residues: 3912 helix: 0.68 (0.15), residues: 1307 sheet: -1.07 (0.22), residues: 563 loop : -1.94 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG d 68 TYR 0.018 0.001 TYR b 833 PHE 0.071 0.002 PHE d 151 TRP 0.014 0.001 TRP a 185 HIS 0.011 0.001 HIS b1015 Details of bonding type rmsd covalent geometry : bond 0.00414 (34167) covalent geometry : angle 0.71750 (46545) hydrogen bonds : bond 0.03927 ( 1260) hydrogen bonds : angle 5.10122 ( 3470) metal coordination : bond 0.01052 ( 30) metal coordination : angle 7.34293 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 360 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 72 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8376 (mp0) REVERT: a 95 PHE cc_start: 0.8269 (m-10) cc_final: 0.7785 (m-10) REVERT: a 108 MET cc_start: 0.8695 (pmm) cc_final: 0.8268 (pmm) REVERT: a 234 MET cc_start: 0.9454 (OUTLIER) cc_final: 0.8603 (ttt) REVERT: a 260 ASP cc_start: 0.8198 (m-30) cc_final: 0.7869 (m-30) REVERT: a 313 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8638 (tp40) REVERT: a 339 ASN cc_start: 0.9264 (t0) cc_final: 0.8827 (t0) REVERT: a 341 MET cc_start: 0.8857 (tpp) cc_final: 0.8195 (tpp) REVERT: a 444 PHE cc_start: 0.8365 (t80) cc_final: 0.7571 (t80) REVERT: a 453 MET cc_start: 0.9280 (mpp) cc_final: 0.8927 (mmm) REVERT: a 455 MET cc_start: 0.7311 (pmm) cc_final: 0.6518 (pmm) REVERT: a 456 MET cc_start: 0.8543 (mpp) cc_final: 0.7396 (mpp) REVERT: a 474 VAL cc_start: 0.9625 (t) cc_final: 0.9252 (p) REVERT: a 515 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8459 (tm-30) REVERT: a 521 MET cc_start: 0.8978 (mmm) cc_final: 0.8205 (mmm) REVERT: a 550 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9129 (tp) REVERT: a 605 MET cc_start: 0.8455 (tpp) cc_final: 0.7366 (mmt) REVERT: a 612 ILE cc_start: 0.9143 (mt) cc_final: 0.8753 (tp) REVERT: a 708 MET cc_start: 0.8040 (mtm) cc_final: 0.7565 (pmm) REVERT: a 1062 GLU cc_start: 0.9386 (tt0) cc_final: 0.9182 (tt0) REVERT: a 1074 GLU cc_start: 0.7886 (tt0) cc_final: 0.7170 (tt0) REVERT: a 1116 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8398 (pp) REVERT: a 1317 MET cc_start: 0.9002 (tmm) cc_final: 0.8728 (tmm) REVERT: a 1400 CYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8528 (p) REVERT: a 1403 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6606 (mm-30) REVERT: b 181 LEU cc_start: 0.9119 (mt) cc_final: 0.8562 (tt) REVERT: b 361 LEU cc_start: 0.9183 (tp) cc_final: 0.8948 (tp) REVERT: b 391 ASP cc_start: 0.9310 (m-30) cc_final: 0.8809 (t0) REVERT: b 412 LEU cc_start: 0.9141 (mt) cc_final: 0.8818 (mt) REVERT: b 481 GLN cc_start: 0.8997 (mt0) cc_final: 0.8164 (mm-40) REVERT: b 542 MET cc_start: 0.9266 (mtp) cc_final: 0.7580 (mtt) REVERT: b 597 MET cc_start: 0.9595 (tpp) cc_final: 0.9057 (tpt) REVERT: b 747 MET cc_start: 0.8974 (mmp) cc_final: 0.8021 (mmp) REVERT: b 834 ASN cc_start: 0.8423 (p0) cc_final: 0.7772 (p0) REVERT: b 1013 ASN cc_start: 0.8690 (t0) cc_final: 0.8406 (t0) REVERT: b 1021 MET cc_start: 0.7882 (mmt) cc_final: 0.7547 (mmp) REVERT: b 1028 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8506 (pp20) REVERT: b 1098 MET cc_start: 0.8273 (mmt) cc_final: 0.7829 (mmt) REVERT: b 1111 MET cc_start: 0.8795 (mmp) cc_final: 0.8583 (tpp) REVERT: b 1193 GLN cc_start: 0.8853 (pt0) cc_final: 0.8413 (pt0) REVERT: b 1201 LYS cc_start: 0.9303 (pptt) cc_final: 0.8996 (ttpp) REVERT: b 1208 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7721 (pmm) REVERT: c 58 LEU cc_start: 0.8883 (mt) cc_final: 0.8151 (tp) REVERT: c 61 GLU cc_start: 0.9276 (pt0) cc_final: 0.9068 (pm20) REVERT: e 22 MET cc_start: 0.9428 (tmm) cc_final: 0.9223 (tmm) REVERT: e 114 ASN cc_start: 0.8945 (m-40) cc_final: 0.8470 (m110) REVERT: f 103 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.9030 (tmm) REVERT: f 104 ASN cc_start: 0.9504 (t0) cc_final: 0.9254 (t0) REVERT: g 22 MET cc_start: 0.9348 (ppp) cc_final: 0.9126 (ppp) REVERT: g 69 GLU cc_start: 0.8908 (tt0) cc_final: 0.8256 (tp30) REVERT: h 89 LEU cc_start: 0.9187 (tt) cc_final: 0.8650 (pt) REVERT: h 97 MET cc_start: 0.8807 (tmm) cc_final: 0.8524 (tmm) REVERT: h 118 PHE cc_start: 0.8977 (m-80) cc_final: 0.8600 (m-80) REVERT: h 123 MET cc_start: 0.8936 (ppp) cc_final: 0.8431 (ppp) REVERT: i 48 LEU cc_start: 0.9469 (tt) cc_final: 0.9210 (pp) REVERT: k 39 ASP cc_start: 0.8844 (t0) cc_final: 0.8609 (t0) REVERT: k 58 PHE cc_start: 0.7837 (t80) cc_final: 0.7610 (t80) REVERT: k 106 GLU cc_start: 0.9795 (tt0) cc_final: 0.9223 (tm-30) REVERT: k 108 GLU cc_start: 0.9351 (tp30) cc_final: 0.8975 (tt0) outliers start: 99 outliers final: 62 residues processed: 429 average time/residue: 0.1879 time to fit residues: 139.5613 Evaluate side-chains 412 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 342 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 124 GLN Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 495 GLU Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 565 ILE Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 649 ILE Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 849 MET Chi-restraints excluded: chain a residue 965 GLN Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1116 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1403 GLU Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 466 TRP Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 748 ILE Chi-restraints excluded: chain b residue 839 MET Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1028 GLU Chi-restraints excluded: chain b residue 1099 VAL Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1162 ILE Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 238 ILE Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain e residue 178 ILE Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 103 MET Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 151 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 102 VAL Chi-restraints excluded: chain i residue 108 HIS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain k residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 74 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 356 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 370 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 215 optimal weight: 5.9990 chunk 391 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 299 HIS ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 587 HIS b 821 GLN ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 195 GLN e 153 HIS ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.074916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049883 restraints weight = 129773.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051934 restraints weight = 60599.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.053326 restraints weight = 37635.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.054259 restraints weight = 27362.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054904 restraints weight = 22144.989| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34197 Z= 0.160 Angle : 0.742 15.855 46581 Z= 0.370 Chirality : 0.044 0.263 5247 Planarity : 0.004 0.053 5704 Dihedral : 16.763 177.916 5419 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 2.85 % Allowed : 20.30 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % 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: -1.32 (0.14), residues: 3912 helix: 0.68 (0.15), residues: 1310 sheet: -0.95 (0.22), residues: 540 loop : -1.96 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 68 TYR 0.025 0.001 TYR b 994 PHE 0.055 0.001 PHE d 151 TRP 0.014 0.001 TRP a 185 HIS 0.016 0.001 HIS a 299 Details of bonding type rmsd covalent geometry : bond 0.00353 (34167) covalent geometry : angle 0.71769 (46545) hydrogen bonds : bond 0.03789 ( 1260) hydrogen bonds : angle 4.97345 ( 3470) metal coordination : bond 0.00923 ( 30) metal coordination : angle 6.84118 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 361 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 72 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8254 (mp0) REVERT: a 95 PHE cc_start: 0.8243 (m-10) cc_final: 0.7737 (m-10) REVERT: a 108 MET cc_start: 0.8711 (pmm) cc_final: 0.8262 (pmm) REVERT: a 234 MET cc_start: 0.9465 (OUTLIER) cc_final: 0.8659 (ttt) REVERT: a 260 ASP cc_start: 0.8054 (m-30) cc_final: 0.7736 (m-30) REVERT: a 313 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8612 (tp40) REVERT: a 339 ASN cc_start: 0.9312 (OUTLIER) cc_final: 0.8881 (t0) REVERT: a 341 MET cc_start: 0.8790 (tpp) cc_final: 0.8077 (tpp) REVERT: a 444 PHE cc_start: 0.8333 (t80) cc_final: 0.7567 (t80) REVERT: a 453 MET cc_start: 0.9242 (mpp) cc_final: 0.8864 (mmm) REVERT: a 455 MET cc_start: 0.7338 (pmm) cc_final: 0.6552 (pmm) REVERT: a 456 MET cc_start: 0.8554 (mpp) cc_final: 0.7552 (mpp) REVERT: a 474 VAL cc_start: 0.9616 (t) cc_final: 0.9246 (p) REVERT: a 515 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8400 (tm-30) REVERT: a 521 MET cc_start: 0.8981 (mmm) cc_final: 0.8192 (mmm) REVERT: a 547 LEU cc_start: 0.9337 (mt) cc_final: 0.8923 (mt) REVERT: a 550 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9136 (tp) REVERT: a 605 MET cc_start: 0.8480 (tpp) cc_final: 0.7871 (tpp) REVERT: a 612 ILE cc_start: 0.9151 (mt) cc_final: 0.8738 (tp) REVERT: a 708 MET cc_start: 0.8000 (mtm) cc_final: 0.7507 (pmm) REVERT: a 1062 GLU cc_start: 0.9395 (tt0) cc_final: 0.9193 (tt0) REVERT: a 1074 GLU cc_start: 0.7839 (tt0) cc_final: 0.7115 (tt0) REVERT: a 1116 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8334 (pp) REVERT: a 1317 MET cc_start: 0.8993 (tmm) cc_final: 0.8694 (tmm) REVERT: a 1375 MET cc_start: 0.9083 (tmm) cc_final: 0.8752 (tmm) REVERT: a 1400 CYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8493 (p) REVERT: a 1403 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6540 (mm-30) REVERT: b 181 LEU cc_start: 0.9100 (mt) cc_final: 0.8532 (tt) REVERT: b 361 LEU cc_start: 0.9177 (tp) cc_final: 0.8942 (tp) REVERT: b 412 LEU cc_start: 0.9125 (mt) cc_final: 0.8800 (mt) REVERT: b 481 GLN cc_start: 0.8972 (mt0) cc_final: 0.8231 (mm-40) REVERT: b 542 MET cc_start: 0.9275 (mtp) cc_final: 0.7626 (mtt) REVERT: b 597 MET cc_start: 0.9590 (tpp) cc_final: 0.9021 (tpt) REVERT: b 747 MET cc_start: 0.8943 (mmp) cc_final: 0.8011 (mmp) REVERT: b 834 ASN cc_start: 0.8148 (p0) cc_final: 0.7358 (m110) REVERT: b 987 LYS cc_start: 0.8481 (ptmt) cc_final: 0.7812 (ptmt) REVERT: b 1021 MET cc_start: 0.7920 (mmt) cc_final: 0.7538 (mmt) REVERT: b 1028 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8561 (pp20) REVERT: b 1098 MET cc_start: 0.8323 (mmt) cc_final: 0.7815 (mmt) REVERT: b 1193 GLN cc_start: 0.8879 (pt0) cc_final: 0.8364 (pt0) REVERT: b 1201 LYS cc_start: 0.9313 (pptt) cc_final: 0.8978 (ttpp) REVERT: b 1208 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7679 (pmm) REVERT: c 58 LEU cc_start: 0.8942 (mt) cc_final: 0.8264 (tp) REVERT: e 22 MET cc_start: 0.9412 (tmm) cc_final: 0.9209 (tmm) REVERT: e 114 ASN cc_start: 0.9007 (m-40) cc_final: 0.8439 (m110) REVERT: f 103 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9019 (tmm) REVERT: f 104 ASN cc_start: 0.9490 (t0) cc_final: 0.9264 (t0) REVERT: f 150 GLU cc_start: 0.9519 (tp30) cc_final: 0.9097 (pt0) REVERT: g 22 MET cc_start: 0.9378 (ppp) cc_final: 0.9144 (ppp) REVERT: h 89 LEU cc_start: 0.9110 (tt) cc_final: 0.8546 (pt) REVERT: h 97 MET cc_start: 0.8777 (tmm) cc_final: 0.8575 (tmm) REVERT: h 118 PHE cc_start: 0.8962 (m-80) cc_final: 0.8579 (m-80) REVERT: h 123 MET cc_start: 0.9011 (ppp) cc_final: 0.8499 (ppp) REVERT: i 48 LEU cc_start: 0.9472 (tt) cc_final: 0.9260 (pp) REVERT: j 58 GLU cc_start: 0.9569 (mm-30) cc_final: 0.8783 (mp0) REVERT: k 1 MET cc_start: 0.9534 (tpp) cc_final: 0.9271 (tpp) REVERT: k 39 ASP cc_start: 0.8900 (t0) cc_final: 0.8663 (t0) REVERT: k 106 GLU cc_start: 0.9789 (tt0) cc_final: 0.9385 (tp30) REVERT: k 108 GLU cc_start: 0.9351 (tp30) cc_final: 0.8960 (tt0) REVERT: l 67 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8462 (m-10) outliers start: 99 outliers final: 66 residues processed: 431 average time/residue: 0.1920 time to fit residues: 142.9722 Evaluate side-chains 425 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 349 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 124 GLN Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 339 ASN Chi-restraints excluded: chain a residue 407 ARG Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 495 GLU Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 649 ILE Chi-restraints excluded: chain a residue 762 SER Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 849 MET Chi-restraints excluded: chain a residue 863 VAL Chi-restraints excluded: chain a residue 965 GLN Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1116 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1403 GLU Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 603 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 748 ILE Chi-restraints excluded: chain b residue 825 VAL Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 999 MET Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1028 GLU Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1162 ILE Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 238 ILE Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain e residue 178 ILE Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 103 MET Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 151 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 84 VAL Chi-restraints excluded: chain i residue 102 VAL Chi-restraints excluded: chain i residue 108 HIS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 31 CYS Chi-restraints excluded: chain l residue 67 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 78 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 157 optimal weight: 0.2980 chunk 129 optimal weight: 20.0000 chunk 247 optimal weight: 0.0470 chunk 264 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 279 optimal weight: 7.9990 overall best weight: 3.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 124 GLN ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.075328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050198 restraints weight = 129113.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.052255 restraints weight = 60495.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.053637 restraints weight = 37645.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054574 restraints weight = 27394.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.055212 restraints weight = 22201.595| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34197 Z= 0.145 Angle : 0.738 15.436 46581 Z= 0.367 Chirality : 0.044 0.264 5247 Planarity : 0.004 0.058 5704 Dihedral : 16.726 177.523 5419 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 2.77 % Allowed : 20.79 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % 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: -1.27 (0.14), residues: 3912 helix: 0.71 (0.15), residues: 1308 sheet: -0.93 (0.22), residues: 551 loop : -1.92 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG f 119 TYR 0.019 0.001 TYR h 116 PHE 0.046 0.001 PHE d 151 TRP 0.013 0.001 TRP a 185 HIS 0.008 0.001 HIS b1015 Details of bonding type rmsd covalent geometry : bond 0.00322 (34167) covalent geometry : angle 0.71744 (46545) hydrogen bonds : bond 0.03688 ( 1260) hydrogen bonds : angle 4.88354 ( 3470) metal coordination : bond 0.00827 ( 30) metal coordination : angle 6.32336 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 363 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 72 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8138 (mp0) REVERT: a 95 PHE cc_start: 0.8252 (m-10) cc_final: 0.7756 (m-10) REVERT: a 108 MET cc_start: 0.8712 (pmm) cc_final: 0.8249 (pmm) REVERT: a 234 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.8696 (ttt) REVERT: a 313 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8582 (tp40) REVERT: a 339 ASN cc_start: 0.9307 (OUTLIER) cc_final: 0.8889 (t0) REVERT: a 453 MET cc_start: 0.9279 (mpp) cc_final: 0.8921 (mmm) REVERT: a 455 MET cc_start: 0.7245 (pmm) cc_final: 0.6473 (pmm) REVERT: a 456 MET cc_start: 0.8566 (mpp) cc_final: 0.7529 (mpp) REVERT: a 474 VAL cc_start: 0.9602 (t) cc_final: 0.9221 (p) REVERT: a 515 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8354 (tm-30) REVERT: a 521 MET cc_start: 0.8981 (mmm) cc_final: 0.8251 (mmm) REVERT: a 547 LEU cc_start: 0.9386 (mt) cc_final: 0.9014 (mt) REVERT: a 605 MET cc_start: 0.8295 (tpp) cc_final: 0.7653 (tpp) REVERT: a 612 ILE cc_start: 0.9154 (mt) cc_final: 0.8788 (tp) REVERT: a 1074 GLU cc_start: 0.7790 (tt0) cc_final: 0.7064 (tt0) REVERT: a 1116 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8318 (pp) REVERT: a 1317 MET cc_start: 0.8977 (tmm) cc_final: 0.8667 (tmm) REVERT: a 1375 MET cc_start: 0.9022 (tmm) cc_final: 0.8718 (tmm) REVERT: a 1400 CYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8445 (p) REVERT: a 1403 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6592 (mm-30) REVERT: a 1454 MET cc_start: 0.7045 (mpp) cc_final: 0.6844 (pmm) REVERT: b 239 GLU cc_start: 0.8730 (tp30) cc_final: 0.8302 (tm-30) REVERT: b 361 LEU cc_start: 0.9171 (tp) cc_final: 0.8929 (tp) REVERT: b 412 LEU cc_start: 0.9117 (mt) cc_final: 0.8810 (mt) REVERT: b 481 GLN cc_start: 0.8977 (mt0) cc_final: 0.8230 (mm-40) REVERT: b 542 MET cc_start: 0.9232 (mtp) cc_final: 0.7525 (mtt) REVERT: b 597 MET cc_start: 0.9574 (tpp) cc_final: 0.9007 (tpt) REVERT: b 684 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9143 (tt) REVERT: b 747 MET cc_start: 0.8917 (mmp) cc_final: 0.7936 (mmp) REVERT: b 834 ASN cc_start: 0.8197 (p0) cc_final: 0.7499 (m110) REVERT: b 987 LYS cc_start: 0.8539 (ptmt) cc_final: 0.7880 (ptmt) REVERT: b 1021 MET cc_start: 0.7924 (mmt) cc_final: 0.7455 (mmt) REVERT: b 1072 MET cc_start: 0.8072 (tpt) cc_final: 0.7112 (tpt) REVERT: b 1081 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8881 (mp) REVERT: b 1098 MET cc_start: 0.8403 (mmt) cc_final: 0.7902 (mmt) REVERT: b 1117 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6867 (mm-40) REVERT: b 1152 MET cc_start: 0.8188 (tpp) cc_final: 0.7969 (mmm) REVERT: b 1193 GLN cc_start: 0.8904 (pt0) cc_final: 0.8411 (pt0) REVERT: b 1201 LYS cc_start: 0.9308 (pptt) cc_final: 0.9002 (tmmt) REVERT: b 1208 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7634 (pmm) REVERT: c 58 LEU cc_start: 0.8950 (mt) cc_final: 0.8282 (tp) REVERT: e 22 MET cc_start: 0.9447 (tmm) cc_final: 0.9225 (tmm) REVERT: e 93 MET cc_start: 0.9459 (ppp) cc_final: 0.9159 (ppp) REVERT: e 114 ASN cc_start: 0.8905 (m-40) cc_final: 0.8419 (m110) REVERT: e 172 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8713 (tm-30) REVERT: f 85 MET cc_start: 0.8194 (tmm) cc_final: 0.7922 (tmm) REVERT: f 103 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.9018 (tmm) REVERT: f 150 GLU cc_start: 0.9541 (tp30) cc_final: 0.9102 (pt0) REVERT: g 22 MET cc_start: 0.9384 (ppp) cc_final: 0.9144 (ppp) REVERT: h 123 MET cc_start: 0.9061 (ppp) cc_final: 0.8767 (ppp) REVERT: i 87 GLN cc_start: 0.7957 (pp30) cc_final: 0.7677 (pp30) REVERT: j 58 GLU cc_start: 0.9582 (mm-30) cc_final: 0.8817 (mp0) REVERT: k 39 ASP cc_start: 0.8917 (t0) cc_final: 0.8661 (t0) REVERT: k 106 GLU cc_start: 0.9764 (tt0) cc_final: 0.9393 (tp30) REVERT: k 108 GLU cc_start: 0.9366 (tp30) cc_final: 0.8973 (tt0) outliers start: 96 outliers final: 69 residues processed: 431 average time/residue: 0.2038 time to fit residues: 150.2292 Evaluate side-chains 424 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 346 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 124 GLN Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 339 ASN Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 407 ARG Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 495 GLU Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 649 ILE Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 849 MET Chi-restraints excluded: chain a residue 863 VAL Chi-restraints excluded: chain a residue 965 GLN Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1116 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1403 GLU Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 466 TRP Chi-restraints excluded: chain b residue 603 LEU Chi-restraints excluded: chain b residue 651 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1081 LEU Chi-restraints excluded: chain b residue 1099 VAL Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1162 ILE Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1182 CYS Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1207 LEU Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain e residue 202 SER Chi-restraints excluded: chain e residue 203 GLU Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 103 MET Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 84 VAL Chi-restraints excluded: chain i residue 108 HIS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 31 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 380 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 371 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 23 optimal weight: 0.0170 chunk 293 optimal weight: 40.0000 chunk 281 optimal weight: 0.6980 chunk 256 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 415 GLN b 821 GLN ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.075266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.050023 restraints weight = 130123.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.052079 restraints weight = 61823.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.053483 restraints weight = 38686.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.054414 restraints weight = 28245.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055041 restraints weight = 22938.086| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34197 Z= 0.133 Angle : 0.754 17.627 46581 Z= 0.372 Chirality : 0.044 0.246 5247 Planarity : 0.004 0.069 5704 Dihedral : 16.690 177.018 5419 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 2.13 % Allowed : 21.71 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % 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: -1.22 (0.14), residues: 3912 helix: 0.75 (0.15), residues: 1309 sheet: -0.86 (0.22), residues: 548 loop : -1.90 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG c 148 TYR 0.023 0.001 TYR b 994 PHE 0.046 0.001 PHE d 151 TRP 0.012 0.001 TRP a 185 HIS 0.007 0.001 HIS c 167 Details of bonding type rmsd covalent geometry : bond 0.00296 (34167) covalent geometry : angle 0.73049 (46545) hydrogen bonds : bond 0.03596 ( 1260) hydrogen bonds : angle 4.83025 ( 3470) metal coordination : bond 0.00732 ( 30) metal coordination : angle 6.74893 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 380 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 72 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8214 (mp0) REVERT: a 95 PHE cc_start: 0.8219 (m-10) cc_final: 0.7710 (m-10) REVERT: a 108 MET cc_start: 0.8704 (pmm) cc_final: 0.8244 (pmm) REVERT: a 234 MET cc_start: 0.9463 (OUTLIER) cc_final: 0.8693 (ttt) REVERT: a 304 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.9006 (tpp) REVERT: a 313 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8445 (tp40) REVERT: a 339 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8857 (t0) REVERT: a 453 MET cc_start: 0.9289 (mpp) cc_final: 0.8934 (mmm) REVERT: a 455 MET cc_start: 0.7294 (pmm) cc_final: 0.6465 (pmm) REVERT: a 456 MET cc_start: 0.8545 (mpp) cc_final: 0.7515 (mpp) REVERT: a 474 VAL cc_start: 0.9573 (t) cc_final: 0.9179 (p) REVERT: a 515 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8313 (tm-30) REVERT: a 521 MET cc_start: 0.8958 (mmm) cc_final: 0.8213 (mmm) REVERT: a 547 LEU cc_start: 0.9378 (mt) cc_final: 0.8980 (mt) REVERT: a 605 MET cc_start: 0.8125 (tpp) cc_final: 0.7507 (tpp) REVERT: a 612 ILE cc_start: 0.9156 (mt) cc_final: 0.8770 (tp) REVERT: a 708 MET cc_start: 0.7559 (pmm) cc_final: 0.7111 (pmm) REVERT: a 1116 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8238 (pp) REVERT: a 1317 MET cc_start: 0.8958 (tmm) cc_final: 0.8643 (tmm) REVERT: a 1364 ASN cc_start: 0.8780 (t0) cc_final: 0.8478 (t0) REVERT: a 1375 MET cc_start: 0.8973 (tmm) cc_final: 0.8692 (tmm) REVERT: a 1400 CYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8468 (p) REVERT: a 1403 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6487 (mm-30) REVERT: a 1430 LEU cc_start: 0.8501 (tp) cc_final: 0.8078 (tp) REVERT: b 239 GLU cc_start: 0.8684 (tp30) cc_final: 0.8277 (tm-30) REVERT: b 361 LEU cc_start: 0.9146 (tp) cc_final: 0.8855 (tp) REVERT: b 412 LEU cc_start: 0.9141 (mt) cc_final: 0.8870 (mt) REVERT: b 521 LEU cc_start: 0.9441 (tp) cc_final: 0.9152 (mm) REVERT: b 542 MET cc_start: 0.9188 (mtp) cc_final: 0.7462 (mtt) REVERT: b 597 MET cc_start: 0.9564 (tpp) cc_final: 0.8997 (tpt) REVERT: b 684 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9144 (tt) REVERT: b 747 MET cc_start: 0.8909 (mmp) cc_final: 0.7870 (mmp) REVERT: b 834 ASN cc_start: 0.8111 (p0) cc_final: 0.7383 (m110) REVERT: b 846 ILE cc_start: 0.9486 (mm) cc_final: 0.9285 (tt) REVERT: b 987 LYS cc_start: 0.8511 (ptmt) cc_final: 0.7847 (ptmt) REVERT: b 999 MET cc_start: 0.8172 (mtt) cc_final: 0.7862 (mmt) REVERT: b 1021 MET cc_start: 0.7916 (mmt) cc_final: 0.7436 (mmp) REVERT: b 1081 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8912 (mp) REVERT: b 1098 MET cc_start: 0.8412 (mmt) cc_final: 0.7913 (mmt) REVERT: b 1117 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6825 (mm-40) REVERT: b 1152 MET cc_start: 0.8231 (tpp) cc_final: 0.8015 (mmm) REVERT: b 1193 GLN cc_start: 0.8881 (pt0) cc_final: 0.8406 (pt0) REVERT: b 1201 LYS cc_start: 0.9198 (pptt) cc_final: 0.8865 (tmmt) REVERT: b 1204 PHE cc_start: 0.8850 (m-80) cc_final: 0.8426 (m-10) REVERT: b 1208 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7611 (pmm) REVERT: c 58 LEU cc_start: 0.8927 (mt) cc_final: 0.8234 (tp) REVERT: c 61 GLU cc_start: 0.9153 (pt0) cc_final: 0.8923 (pm20) REVERT: c 69 LEU cc_start: 0.9599 (mp) cc_final: 0.9367 (mp) REVERT: d 145 MET cc_start: 0.8385 (tpt) cc_final: 0.8075 (tpp) REVERT: e 22 MET cc_start: 0.9483 (tmm) cc_final: 0.9263 (tmm) REVERT: e 93 MET cc_start: 0.9453 (ppp) cc_final: 0.9144 (ppp) REVERT: e 114 ASN cc_start: 0.8976 (m-40) cc_final: 0.8444 (m110) REVERT: e 172 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8674 (tm-30) REVERT: f 85 MET cc_start: 0.8223 (tmm) cc_final: 0.7972 (tmm) REVERT: f 103 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8885 (tmm) REVERT: f 150 GLU cc_start: 0.9501 (tp30) cc_final: 0.8973 (pt0) REVERT: g 22 MET cc_start: 0.9377 (ppp) cc_final: 0.9107 (ppp) REVERT: h 118 PHE cc_start: 0.9008 (m-80) cc_final: 0.8600 (m-10) REVERT: h 123 MET cc_start: 0.9025 (ppp) cc_final: 0.8494 (ppp) REVERT: i 48 LEU cc_start: 0.9327 (tt) cc_final: 0.9062 (pp) REVERT: i 87 GLN cc_start: 0.7927 (pp30) cc_final: 0.7654 (pp30) REVERT: j 28 ASP cc_start: 0.8919 (m-30) cc_final: 0.8582 (m-30) REVERT: j 58 GLU cc_start: 0.9562 (mm-30) cc_final: 0.8778 (mp0) REVERT: k 39 ASP cc_start: 0.8919 (t0) cc_final: 0.8654 (t0) REVERT: k 106 GLU cc_start: 0.9743 (tt0) cc_final: 0.9382 (tp30) REVERT: k 108 GLU cc_start: 0.9375 (tp30) cc_final: 0.8986 (tt0) REVERT: l 67 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8253 (m-10) outliers start: 74 outliers final: 56 residues processed: 429 average time/residue: 0.1870 time to fit residues: 139.0245 Evaluate side-chains 425 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 358 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 304 MET Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 339 ASN Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 407 ARG Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 495 GLU Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 658 LEU Chi-restraints excluded: chain a residue 762 SER Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 849 MET Chi-restraints excluded: chain a residue 863 VAL Chi-restraints excluded: chain a residue 965 GLN Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1116 LEU Chi-restraints excluded: chain a residue 1195 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1403 GLU Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 603 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1081 LEU Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain e residue 202 SER Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 103 MET Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain h residue 97 MET Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 84 VAL Chi-restraints excluded: chain i residue 108 HIS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 31 CYS Chi-restraints excluded: chain l residue 67 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 44 optimal weight: 0.0870 chunk 29 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 369 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 124 GLN ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 306 ASN ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.075156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050167 restraints weight = 130613.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.052202 restraints weight = 61735.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053588 restraints weight = 38509.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.054534 restraints weight = 28064.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.055146 restraints weight = 22666.493| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34197 Z= 0.161 Angle : 0.764 17.996 46581 Z= 0.378 Chirality : 0.044 0.255 5247 Planarity : 0.004 0.071 5704 Dihedral : 16.715 176.504 5419 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 2.25 % Allowed : 21.60 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % 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: -1.23 (0.14), residues: 3912 helix: 0.75 (0.15), residues: 1314 sheet: -0.92 (0.22), residues: 560 loop : -1.91 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 148 TYR 0.021 0.001 TYR h 102 PHE 0.044 0.001 PHE d 151 TRP 0.024 0.001 TRP b 31 HIS 0.008 0.001 HIS b1015 Details of bonding type rmsd covalent geometry : bond 0.00359 (34167) covalent geometry : angle 0.74062 (46545) hydrogen bonds : bond 0.03704 ( 1260) hydrogen bonds : angle 4.86768 ( 3470) metal coordination : bond 0.00935 ( 30) metal coordination : angle 6.81417 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 354 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 72 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8244 (mp0) REVERT: a 95 PHE cc_start: 0.8250 (m-10) cc_final: 0.7744 (m-10) REVERT: a 108 MET cc_start: 0.8699 (pmm) cc_final: 0.8267 (pmm) REVERT: a 234 MET cc_start: 0.9467 (OUTLIER) cc_final: 0.8710 (ttt) REVERT: a 304 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.9002 (tpp) REVERT: a 313 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8434 (tp40) REVERT: a 339 ASN cc_start: 0.9276 (OUTLIER) cc_final: 0.9014 (t0) REVERT: a 453 MET cc_start: 0.9263 (mpp) cc_final: 0.8972 (mmm) REVERT: a 455 MET cc_start: 0.7340 (pmm) cc_final: 0.6527 (pmm) REVERT: a 456 MET cc_start: 0.8599 (mpp) cc_final: 0.7573 (mpp) REVERT: a 474 VAL cc_start: 0.9585 (t) cc_final: 0.9185 (p) REVERT: a 515 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8361 (tm-30) REVERT: a 521 MET cc_start: 0.9007 (mmm) cc_final: 0.8244 (mmm) REVERT: a 605 MET cc_start: 0.8147 (tpp) cc_final: 0.7542 (tpp) REVERT: a 612 ILE cc_start: 0.9162 (mt) cc_final: 0.8797 (tp) REVERT: a 708 MET cc_start: 0.7485 (pmm) cc_final: 0.7075 (pmm) REVERT: a 853 ASP cc_start: 0.9434 (t0) cc_final: 0.8785 (t70) REVERT: a 1116 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8304 (pp) REVERT: a 1317 MET cc_start: 0.8948 (tmm) cc_final: 0.8631 (tmm) REVERT: a 1364 ASN cc_start: 0.8854 (t0) cc_final: 0.8565 (t0) REVERT: a 1375 MET cc_start: 0.8978 (tmm) cc_final: 0.8644 (tmm) REVERT: a 1400 CYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8510 (p) REVERT: a 1403 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6512 (mm-30) REVERT: a 1430 LEU cc_start: 0.8534 (tp) cc_final: 0.8096 (tp) REVERT: b 239 GLU cc_start: 0.8701 (tp30) cc_final: 0.8270 (tm-30) REVERT: b 361 LEU cc_start: 0.9167 (tp) cc_final: 0.8929 (tp) REVERT: b 412 LEU cc_start: 0.9118 (mt) cc_final: 0.8818 (mt) REVERT: b 542 MET cc_start: 0.9261 (mtp) cc_final: 0.8940 (mtp) REVERT: b 597 MET cc_start: 0.9576 (tpp) cc_final: 0.9013 (tpt) REVERT: b 684 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9142 (tt) REVERT: b 705 MET cc_start: 0.8468 (tmm) cc_final: 0.8080 (tpp) REVERT: b 834 ASN cc_start: 0.8194 (p0) cc_final: 0.7532 (m110) REVERT: b 987 LYS cc_start: 0.8560 (ptmt) cc_final: 0.7959 (ptmt) REVERT: b 999 MET cc_start: 0.8190 (mtt) cc_final: 0.7849 (mmt) REVERT: b 1021 MET cc_start: 0.7891 (mmt) cc_final: 0.7416 (mmp) REVERT: b 1072 MET cc_start: 0.8075 (tpt) cc_final: 0.7286 (tpt) REVERT: b 1081 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8850 (mp) REVERT: b 1098 MET cc_start: 0.8423 (mmt) cc_final: 0.7896 (mmt) REVERT: b 1117 GLN cc_start: 0.7294 (mm-40) cc_final: 0.6882 (mm-40) REVERT: b 1152 MET cc_start: 0.8238 (tpp) cc_final: 0.8023 (mmm) REVERT: b 1193 GLN cc_start: 0.8905 (pt0) cc_final: 0.8431 (pt0) REVERT: b 1201 LYS cc_start: 0.9225 (pptt) cc_final: 0.8886 (ttpp) REVERT: b 1208 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7627 (pmm) REVERT: c 58 LEU cc_start: 0.8923 (mt) cc_final: 0.8233 (tp) REVERT: e 22 MET cc_start: 0.9459 (tmm) cc_final: 0.9229 (tmm) REVERT: e 114 ASN cc_start: 0.8991 (m-40) cc_final: 0.8463 (m110) REVERT: e 172 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8703 (tm-30) REVERT: f 85 MET cc_start: 0.8373 (tmm) cc_final: 0.8085 (tmm) REVERT: f 103 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8904 (tmm) REVERT: f 127 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8551 (tm-30) REVERT: f 149 GLU cc_start: 0.8942 (pm20) cc_final: 0.8399 (pm20) REVERT: f 150 GLU cc_start: 0.9478 (tp30) cc_final: 0.9178 (mp0) REVERT: g 1 MET cc_start: 0.8793 (pmm) cc_final: 0.8462 (pmm) REVERT: g 22 MET cc_start: 0.9382 (ppp) cc_final: 0.9149 (ppp) REVERT: g 64 THR cc_start: 0.9361 (t) cc_final: 0.9108 (p) REVERT: h 118 PHE cc_start: 0.9067 (m-80) cc_final: 0.8629 (m-10) REVERT: h 123 MET cc_start: 0.9037 (ppp) cc_final: 0.8485 (ppp) REVERT: i 48 LEU cc_start: 0.9343 (tt) cc_final: 0.9094 (pp) REVERT: i 62 ILE cc_start: 0.9498 (tp) cc_final: 0.9225 (mm) REVERT: j 28 ASP cc_start: 0.8979 (m-30) cc_final: 0.8675 (m-30) REVERT: j 58 GLU cc_start: 0.9574 (mm-30) cc_final: 0.8787 (mp0) REVERT: k 39 ASP cc_start: 0.8944 (t0) cc_final: 0.8682 (t0) REVERT: k 106 GLU cc_start: 0.9740 (tt0) cc_final: 0.9381 (tp30) REVERT: k 108 GLU cc_start: 0.9359 (tp30) cc_final: 0.8983 (tt0) REVERT: l 67 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8317 (m-10) outliers start: 78 outliers final: 62 residues processed: 408 average time/residue: 0.1919 time to fit residues: 135.7818 Evaluate side-chains 420 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 347 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 124 GLN Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 304 MET Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 339 ASN Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 407 ARG Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 495 GLU Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 762 SER Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 849 MET Chi-restraints excluded: chain a residue 863 VAL Chi-restraints excluded: chain a residue 965 GLN Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1116 LEU Chi-restraints excluded: chain a residue 1195 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1403 GLU Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 603 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1028 GLU Chi-restraints excluded: chain b residue 1081 LEU Chi-restraints excluded: chain b residue 1099 VAL Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain d residue 165 GLN Chi-restraints excluded: chain e residue 202 SER Chi-restraints excluded: chain e residue 203 GLU Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 103 MET Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain h residue 97 MET Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 84 VAL Chi-restraints excluded: chain i residue 108 HIS Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 31 CYS Chi-restraints excluded: chain l residue 67 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 356 optimal weight: 7.9990 chunk 398 optimal weight: 40.0000 chunk 384 optimal weight: 7.9990 chunk 311 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 382 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.074220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048984 restraints weight = 134165.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050985 restraints weight = 64720.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.052347 restraints weight = 40906.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.053241 restraints weight = 30083.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.053838 restraints weight = 24573.199| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 34197 Z= 0.189 Angle : 0.853 59.194 46581 Z= 0.442 Chirality : 0.044 0.424 5247 Planarity : 0.004 0.067 5704 Dihedral : 16.716 176.503 5419 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 2.34 % Allowed : 21.60 % Favored : 76.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % 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: -1.24 (0.14), residues: 3912 helix: 0.74 (0.15), residues: 1314 sheet: -0.92 (0.22), residues: 560 loop : -1.91 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG k 54 TYR 0.051 0.001 TYR a 551 PHE 0.044 0.001 PHE d 151 TRP 0.021 0.001 TRP b 31 HIS 0.007 0.001 HIS b1015 Details of bonding type rmsd covalent geometry : bond 0.00408 (34167) covalent geometry : angle 0.83195 (46545) hydrogen bonds : bond 0.03711 ( 1260) hydrogen bonds : angle 4.86823 ( 3470) metal coordination : bond 0.00915 ( 30) metal coordination : angle 6.80331 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7418.61 seconds wall clock time: 128 minutes 44.61 seconds (7724.61 seconds total)